Citrus Sinensis ID: 040338

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-----
Protein Sequence
MKACGSLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHcccccHHcccHHHHHHHHccccccccEEHHHHHHHHHHccccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHHHccccccccHHHHHHHHHHHHccccccccccHHHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccHHHHHHHHHHHcccccccccHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccccccccHHHHHHHHHHcccccHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHcccccEEEHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEccHHHHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
mkacgslkslPIARKIHAQLISTCLISSIFLQLIdddyrvfcdigprylftYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMlnpslfcwKFGIIRLLIMFQkmperdlvSWNTMISILTRHGFGFETLCTFIELwnhgfglsSMLYATAFSARASvydlewgphlhsrvvhmepsldvfvgsGLIDMYLKcgcngiesSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSqagvlekprFFFFFVSLLsgcshsgpvtkgkHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLidempskptcVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS
Flexible Loop (DISEMBL)
mkacgslkSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS
Low Complexity Region (SEG)
MKACGSLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS
Disordered region (IsUnstruct)
********SLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF**
Disordered Region (DISOPRED)
MKACGS*KSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQ*DVK****
Disordered Region (DISEMBL)
MKACGSLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS
Disordered Region (DISPRO)
MKACGSLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLD******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKACGSLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS
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	385	2.2.26 [Sep-21-2011]
Q9SIT7	697	Pentatricopeptide repeat-	yes	no	0.932	0.515	0.269	1e-36
Q9SY02	781	Pentatricopeptide repeat-	no	no	0.807	0.398	0.286	1e-35
Q9FI80	646	Pentatricopeptide repeat-	no	no	0.872	0.520	0.275	1e-34
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.828	0.514	0.304	1e-34
Q56XI1	705	Pentatricopeptide repeat-	no	no	0.831	0.453	0.274	2e-32
Q9LXE8	623	Pentatricopeptide repeat-	no	no	0.766	0.473	0.292	4e-32
Q9C8L6	717	Pentatricopeptide repeat-	no	no	0.618	0.331	0.336	5e-32
O82380	738	Pentatricopeptide repeat-	no	no	0.942	0.491	0.239	7e-32
Q9S7F4	825	Putative pentatricopeptid	no	no	0.641	0.299	0.298	1e-31
Q9MA85	658	Pentatricopeptide repeat-	no	no	0.820	0.480	0.280	4e-31

>sp|Q9SIT7|PP151_ARATH Pentatricopeptide repeat-containing protein At2g13600 OS=Arabidopsis thaliana GN=PCMP-E76 PE=3 SV=1

 Score =  154 bits (389), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 122/453 (26%), Positives = 196/453 (43%), Gaps = 94/453 (20%)

Query: 1   MKACGSLKSLPIARKIHAQLISTCLISSIFL--QLID---------DDYRVFCDIGPRYL 49
           + AC  L  +    ++H+ +  +  +S +++   L+D         D  RVF ++G R +
Sbjct: 159 LSACSGLNDMNKGVQVHSLIAKSPFLSDVYIGSALVDMYSKCGNVNDAQRVFDEMGDRNV 218

Query: 50  FTYNTMI-----NGGV---------------------------RCLCVGNIKMALHLHG- 76
            ++N++I     NG                              C  +  IK+   +HG 
Sbjct: 219 VSWNSLITCFEQNGPAVEALDVFQMMLESRVEPDEVTLASVISACASLSAIKVGQEVHGR 278

Query: 77  LVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL---------FCWKFGIIR 127
           +VK     +D  ++ + +DM+ KC  +  A   F  M   ++         +        
Sbjct: 279 VVKNDKLRNDIILSNAFVDMYAKCSRIKEARFIFDSMPIRNVIAETSMISGYAMAASTKA 338

Query: 128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS 187
             +MF KM ER++VSWN +I+  T++G   E L  F  L       +   +A    A A 
Sbjct: 339 ARLMFTKMAERNVVSWNALIAGYTQNGENEEALSLFCLLKRESVCPTHYSFANILKACAD 398

Query: 188 VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG---CNGIESSIQIGKALVTMYAE 244
           + +L  G   H  V                   LK G    +G E  I +G +L+ MY +
Sbjct: 399 LAELHLGMQAHVHV-------------------LKHGFKFQSGEEDDIFVGNSLIDMYVK 439

Query: 245 GGSTQKADLAFELMSRRNMISWMVLISAFSQAGVL--------------EKPRFFFFFVS 290
            G  ++  L F  M  R+ +SW  +I  F+Q G                EKP      + 
Sbjct: 440 CGCVEEGYLVFRKMMERDCVSWNAMIIGFAQNGYGNEALELFREMLESGEKPDHITM-IG 498

Query: 291 LLSGCSHSGPVTKGKHYFTAMAK----FTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSK 346
           +LS C H+G V +G+HYF++M +         ++ CMVDLLG +G L EAK +I+EMP +
Sbjct: 499 VLSACGHAGFVEEGRHYFSSMTRDFGVAPLRDHYTCMVDLLGRAGFLEEAKSMIEEMPMQ 558

Query: 347 PTCVIWGALLGACCSHYNTKLAELVMRNLLQLD 379
           P  VIWG+LL AC  H N  L + V   LL+++
Sbjct: 559 PDSVIWGSLLAACKVHRNITLGKYVAEKLLEVE 591

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SY02|PP301_ARATH Pentatricopeptide repeat-containing protein At4g02750 OS=Arabidopsis thaliana GN=PCMP-H24 PE=3 SV=1

 Score =  150 bits (380), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 109/380 (28%), Positives = 178/380 (46%), Gaps = 69/380 (18%)

Query: 23  TCLISS-IFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF 81
           T ++S  I  +++++   +F  +  R   ++N M+ G V+      ++MA  L  ++   
Sbjct: 285 TAMVSGYIQNRMVEEARELFDKMPERNEVSWNAMLAGYVQG---ERMEMAKELFDVMP-- 339

Query: 82  YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLV 141
               + S   + I  + +CG +  A++                      +F KMP+RD V
Sbjct: 340 --CRNVSTWNTMITGYAQCGKISEAKN----------------------LFDKMPKRDPV 375

Query: 142 SWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRV 201
           SW  MI+  ++ G  FE L  F+++   G  L+   +++A S  A V  LE G  LH R+
Sbjct: 376 SWAAMIAGYSQSGHSFEALRLFVQMEREGGRLNRSSFSSALSTCADVVALELGKQLHGRL 435

Query: 202 VHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR 261
           V        FVG+ L+ MY KC                      GS ++A+  F+ M+ +
Sbjct: 436 VKGGYETGCFVGNALLLMYCKC----------------------GSIEEANDLFKEMAGK 473

Query: 262 NMISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKHYF 308
           +++SW  +I+ +S+ G  E    FF               V++LS CSH+G V KG+ YF
Sbjct: 474 DIVSWNTMIAGYSRHGFGEVALRFFESMKREGLKPDDATMVAVLSACSHTGLVDKGRQYF 533

Query: 309 TAMAK----FTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYN 364
             M +       + ++ CMVDLLG +GLL +A  L+  MP +P   IWG LLGA   H N
Sbjct: 534 YTMTQDYGVMPNSQHYACMVDLLGRAGLLEDAHNLMKNMPFEPDAAIWGTLLGASRVHGN 593

Query: 365 TKLAELVMRNLLQLDVKVFG 384
           T+LAE     +  ++ +  G
Sbjct: 594 TELAETAADKIFAMEPENSG 613

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FI80|PP425_ARATH Pentatricopeptide repeat-containing protein At5g48910 OS=Arabidopsis thaliana GN=PCMP-H38 PE=2 SV=1

 Score =  147 bits (372), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 121/439 (27%), Positives = 185/439 (42%), Gaps = 103/439 (23%)

Query: 18  AQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVR---------------- 61
           A+++  C  S +  + +D  +++F  +  R  F++NT+I G                   
Sbjct: 59  AEILRFCATSDLHHRDLDYAHKIFNQMPQRNCFSWNTIIRGFSESDEDKALIAITLFYEM 118

Query: 62  -------------------CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA 102
                              C   G I+    +HGL  K+ F  DE +  + + M+V CG 
Sbjct: 119 MSDEFVEPNRFTFPSVLKACAKTGKIQEGKQIHGLALKYGFGGDEFVMSNLVRMYVMCGF 178

Query: 103 VDYAESAFL--------------RMLNPSLFCWKF---GIIRL------LIMFQKMPERD 139
           +  A   F               R  +  +  W     G +RL       ++F KM +R 
Sbjct: 179 MKDARVLFYKNIIEKDMVVMTDRRKRDGEIVLWNVMIDGYMRLGDCKAARMLFDKMRQRS 238

Query: 140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHS 199
           +VSWNTMIS  + +GF  + +  F E+       + +   +   A + +  LE G  LH 
Sbjct: 239 VVSWNTMISGYSLNGFFKDAVEVFREMKKGDIRPNYVTLVSVLPAISRLGSLELGEWLHL 298

Query: 200 RVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMS 259
                   +D  +GS LIDMY KCG   IE +I +                    FE + 
Sbjct: 299 YAEDSGIRIDDVLGSALIDMYSKCGI--IEKAIHV--------------------FERLP 336

Query: 260 RRNMISWMVLISAFS----------------QAGVLEKPRFFFFFVSLLSGCSHSGPVTK 303
           R N+I+W  +I+ F+                QAGV         +++LL+ CSH G V +
Sbjct: 337 RENVITWSAMINGFAIHGQAGDAIDCFCKMRQAGVRPSD---VAYINLLTACSHGGLVEE 393

Query: 304 GKHYFTAMAKFT----YTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGAC 359
           G+ YF+ M           ++ CMVDLLG SGLL EA++ I  MP KP  VIW ALLGAC
Sbjct: 394 GRRYFSQMVSVDGLEPRIEHYGCMVDLLGRSGLLDEAEEFILNMPIKPDDVIWKALLGAC 453

Query: 360 CSHYNTKLAELVMRNLLQL 378
               N ++ + V   L+ +
Sbjct: 454 RMQGNVEMGKRVANILMDM 472

Arabidopsis thaliana (taxid: 3702)

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

 Score =  147 bits (371), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 111/364 (30%), Positives = 167/364 (45%), Gaps = 45/364 (12%)

Query: 39  RVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHV 98
           R+ C   P   +T+ +++     C  +   +    +H  + K  + +D     S I+ + 
Sbjct: 105 RMLCSSAPHNAYTFPSLLKA---CSNLSAFEETTQIHAQITKLGYENDVYAVNSLINSYA 161

Query: 99  KCGAVDYAESAFLRMLNPSLFCW--------KFGIIRL-LIMFQKMPERDLVSWNTMISI 149
             G    A   F R+  P    W        K G + + L +F+KM E++ +SW TMIS 
Sbjct: 162 VTGNFKLAHLLFDRIPEPDDVSWNSVIKGYVKAGKMDIALTLFRKMAEKNAISWTTMISG 221

Query: 150 LTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLD 209
             +     E L  F E+ N      ++  A A SA A +  LE G  +HS +      +D
Sbjct: 222 YVQADMNKEALQLFHEMQNSDVEPDNVSLANALSACAQLGALEQGKWIHSYLNKTRIRMD 281

Query: 210 VFVGSGLIDMYLKCG---------CNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR 260
             +G  LIDMY KCG          N  + S+Q   AL++ YA  G  ++A   F  M +
Sbjct: 282 SVLGCVLIDMYAKCGEMEEALEVFKNIKKKSVQAWTALISGYAYHGHGREAISKFMEMQK 341

Query: 261 RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTC-- 318
             +                 KP    F  ++L+ CS++G V +GK  F +M +  Y    
Sbjct: 342 MGI-----------------KPNVITF-TAVLTACSYTGLVEEGKLIFYSMER-DYNLKP 382

Query: 319 ---YFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNL 375
              ++ C+VDLLG +GLL EAK+ I EMP KP  VIWGALL AC  H N +L E +   L
Sbjct: 383 TIEHYGCIVDLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRIHKNIELGEEIGEIL 442

Query: 376 LQLD 379
           + +D
Sbjct: 443 IAID 446

Arabidopsis thaliana (taxid: 3702)

>sp|Q56XI1|PPR25_ARATH Pentatricopeptide repeat-containing protein At1g09410 OS=Arabidopsis thaliana GN=PCMP-H18 PE=2 SV=2

 Score =  140 bits (353), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 105/382 (27%), Positives = 175/382 (45%), Gaps = 62/382 (16%)

Query: 34  IDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSS 93
           +D+   +F ++  R + T+ TM+ G  +   V +           +K + V  E    S 
Sbjct: 188 VDEAREIFDEMSERSVITWTTMVTGYGQNNRVDD----------ARKIFDVMPEKTEVSW 237

Query: 94  IDM---HVKCGAVDYAESAFLRM-LNPSLFC--------WKFGIIRLLIMFQKMPERDLV 141
             M   +V+ G ++ AE  F  M + P + C         K  I +   +F  M ER+  
Sbjct: 238 TSMLMGYVQNGRIEDAEELFEVMPVKPVIACNAMISGLGQKGEIAKARRVFDSMKERNDA 297

Query: 142 SWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRV 201
           SW T+I I  R+GF  E L  FI +   G   +     +  S  AS+  L  G  +H+++
Sbjct: 298 SWQTVIKIHERNGFELEALDLFILMQKQGVRPTFPTLISILSVCASLASLHHGKQVHAQL 357

Query: 202 VHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR 261
           V  +  +DV+V S L+ MY+KCG             LV          K+ L F+    +
Sbjct: 358 VRCQFDVDVYVASVLMTMYIKCG------------ELV----------KSKLIFDRFPSK 395

Query: 262 NMISWMVLISAFSQAGVLEKPRFFF--------------FFVSLLSGCSHSGPVTKGKHY 307
           ++I W  +IS ++  G+ E+    F               FV+ LS CS++G V +G   
Sbjct: 396 DIIMWNSIISGYASHGLGEEALKVFCEMPLSGSTKPNEVTFVATLSACSYAGMVEEGLKI 455

Query: 308 FTAMAKF----TYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHY 363
           + +M         T ++ CMVD+LG +G   EA ++ID M  +P   +WG+LLGAC +H 
Sbjct: 456 YESMESVFGVKPITAHYACMVDMLGRAGRFNEAMEMIDSMTVEPDAAVWGSLLGACRTHS 515

Query: 364 NTKLAELVMRNLLQLDVKVFGS 385
              +AE   + L++++ +  G+
Sbjct: 516 QLDVAEFCAKKLIEIEPENSGT 537

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXE8|PP386_ARATH Pentatricopeptide repeat-containing protein At5g15340, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H91 PE=2 SV=1

 Score =  139 bits (350), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 102/349 (29%), Positives = 162/349 (46%), Gaps = 54/349 (15%)

Query: 62  CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW 121
           C  + ++  A   HG+  K   ++   +  + +DM+ KCG V   +  F  +   S+  W
Sbjct: 121 CAKLEDLGFAQQGHGVAVKMGVLTSVKVCNALMDMYGKCGLVSEVKRIFEELEEKSVVSW 180

Query: 122 KF---------GIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL-WNHGF 171
                      G+ R   +F +MPER+ V+W  M++     GF  E L    E+ +  G 
Sbjct: 181 TVVLDTVVKWEGLERGREVFHEMPERNAVAWTVMVAGYLGAGFTREVLELLAEMVFRCGH 240

Query: 172 GLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL-------DVFVGSGLIDMYLKCG 224
           GL+ +   +  SA A   +L  G  +H   +  E  +       DV VG+ L+DMY KCG
Sbjct: 241 GLNFVTLCSMLSACAQSGNLVVGRWVHVYALKKEMMMGEEASYDDVMVGTALVDMYAKCG 300

Query: 225 CNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAG------- 277
              I+SS+ +                    F LM +RN+++W  L S  +  G       
Sbjct: 301 --NIDSSMNV--------------------FRLMRKRNVVTWNALFSGLAMHGKGRMVID 338

Query: 278 -----VLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKF---TYTCYFVCMVDLLGL 329
                + E       F ++LS CSHSG V +G   F ++  +       ++ CMVDLLG 
Sbjct: 339 MFPQMIREVKPDDLTFTAVLSACSHSGIVDEGWRCFHSLRFYGLEPKVDHYACMVDLLGR 398

Query: 330 SGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQL 378
           +GL+ EA+ L+ EMP  P  V+ G+LLG+C  H   ++AE + R L+Q+
Sbjct: 399 AGLIEEAEILMREMPVPPNEVVLGSLLGSCSVHGKVEIAERIKRELIQM 447

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C8L6|PPR80_ARATH Pentatricopeptide repeat-containing protein At1g53600, mitochondrial OS=Arabidopsis thaliana GN=PCMP-E63 PE=2 SV=2

 Score =  139 bits (349), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 94/279 (33%), Positives = 135/279 (48%), Gaps = 41/279 (14%)

Query: 119 FCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLY 178
           F  K  I + + +F  MPE+D ++W  MIS    +G+  E LC F ++       +S  +
Sbjct: 382 FSGKGEISKCVELFGMMPEKDNITWTAMISAFVSNGYYEEALCWFHKMLQKEVCPNSYTF 441

Query: 179 ATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKAL 238
           ++  SA AS+ DL  G  +H RVV M    D+ V + L+ MY KC               
Sbjct: 442 SSVLSATASLADLIEGLQIHGRVVKMNIVNDLSVQNSLVSMYCKC--------------- 486

Query: 239 VTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF------------ 286
                  G+T  A   F  +S  N++S+  +IS +S  G  +K    F            
Sbjct: 487 -------GNTNDAYKIFSCISEPNIVSYNTMISGYSYNGFGKKALKLFSMLESSGKEPNG 539

Query: 287 -FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTC-----YFVCMVDLLGLSGLLGEAKKLI 340
             F++LLS C H G V  G  YF +M K +Y       ++ CMVDLLG SGLL +A  LI
Sbjct: 540 VTFLALLSACVHVGYVDLGWKYFKSM-KSSYNIEPGPDHYACMVDLLGRSGLLDDASNLI 598

Query: 341 DEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLD 379
             MP KP   +WG+LL A  +H    LAEL  + L++L+
Sbjct: 599 STMPCKPHSGVWGSLLSASKTHLRVDLAELAAKKLIELE 637

Arabidopsis thaliana (taxid: 3702)

>sp|O82380|PP175_ARATH Pentatricopeptide repeat-containing protein At2g29760, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H33 PE=2 SV=1

 Score =  138 bits (348), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 109/455 (23%), Positives = 192/455 (42%), Gaps = 92/455 (20%)

Query: 1   MKACGSLKSLPIARKIHAQLISTCLISSIFLQL-----------IDDDYRVFCDIGPRYL 49
           +KA   + SL + + +H   + + + S +F+             +D   +VF  I  + +
Sbjct: 138 IKAAAEVSSLSLGQSLHGMAVKSAVGSDVFVANSLIHCYFSCGDLDSACKVFTTIKEKDV 197

Query: 50  FTYNTMINGGVR--------------------------------CLCVGNIKMALHLHGL 77
            ++N+MING V+                                C  + N++    +   
Sbjct: 198 VSWNSMINGFVQKGSPDKALELFKKMESEDVKASHVTMVGVLSACAKIRNLEFGRQVCSY 257

Query: 78  VKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLI------- 130
           +++     + ++A + +DM+ KCG+++ A+  F  M       W   +    I       
Sbjct: 258 IEENRVNVNLTLANAMLDMYTKCGSIEDAKRLFDAMEEKDNVTWTTMLDGYAISEDYEAA 317

Query: 131 --MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW-NHGFGLSSMLYATAFSARAS 187
             +   MP++D+V+WN +IS   ++G   E L  F EL       L+ +   +  SA A 
Sbjct: 318 REVLNSMPQKDIVAWNALISAYEQNGKPNEALIVFHELQLQKNMKLNQITLVSTLSACAQ 377

Query: 188 VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS 247
           V  LE G  +HS                    Y+K   +GI  +  +  AL+ MY++ G 
Sbjct: 378 VGALELGRWIHS--------------------YIKK--HGIRMNFHVTSALIHMYSKCGD 415

Query: 248 TQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFF-------------FVSLLSG 294
            +K+   F  + +R++  W  +I   +  G   +    F+             F ++   
Sbjct: 416 LEKSREVFNSVEKRDVFVWSAMIGGLAMHGCGNEAVDMFYKMQEANVKPNGVTFTNVFCA 475

Query: 295 CSHSGPVTKGKHYFTAMAK----FTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCV 350
           CSH+G V + +  F  M           ++ C+VD+LG SG L +A K I+ MP  P+  
Sbjct: 476 CSHTGLVDEAESLFHQMESNYGIVPEEKHYACIVDVLGRSGYLEKAVKFIEAMPIPPSTS 535

Query: 351 IWGALLGACCSHYNTKLAELVMRNLLQLDVKVFGS 385
           +WGALLGAC  H N  LAE+    LL+L+ +  G+
Sbjct: 536 VWGALLGACKIHANLNLAEMACTRLLELEPRNDGA 570

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S7F4|PP206_ARATH Putative pentatricopeptide repeat-containing protein At2g01510 OS=Arabidopsis thaliana GN=PCMP-H36 PE=3 SV=1

 Score =  137 bits (345), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 92/308 (29%), Positives = 135/308 (43%), Gaps = 61/308 (19%)

Query: 89  IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMIS 148
           +  S +DM+ KC   + AE                      ++F+ +P+R  VSW  +IS
Sbjct: 388 VGNSLVDMYAKCEMFEEAE----------------------LIFKSLPQRTTVSWTALIS 425

Query: 149 ILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL 208
              + G     L  F ++           +AT   A AS   L  G  LH+ ++      
Sbjct: 426 GYVQKGLHGAGLKLFTKMRGSNLRADQSTFATVLKASASFASLLLGKQLHAFIIRSGNLE 485

Query: 209 DVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMV 268
           +VF GSGL+DMY KCG   I+ ++Q+                    FE M  RN +SW  
Sbjct: 486 NVFSGSGLVDMYAKCG--SIKDAVQV--------------------FEEMPDRNAVSWNA 523

Query: 269 LISAFSQAGVLEKPRFFFF-------------FVSLLSGCSHSGPVTKGKHYFTAMAKF- 314
           LISA +  G  E     F               + +L+ CSH G V +G  YF AM+   
Sbjct: 524 LISAHADNGDGEAAIGAFAKMIESGLQPDSVSILGVLTACSHCGFVEQGTEYFQAMSPIY 583

Query: 315 ---TYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELV 371
                  ++ CM+DLLG +G   EA+KL+DEMP +P  ++W ++L AC  H N  LAE  
Sbjct: 584 GITPKKKHYACMLDLLGRNGRFAEAEKLMDEMPFEPDEIMWSSVLNACRIHKNQSLAERA 643

Query: 372 MRNLLQLD 379
              L  ++
Sbjct: 644 AEKLFSME 651

Arabidopsis thaliana (taxid: 3702)

>sp|Q9MA85|PP215_ARATH Pentatricopeptide repeat-containing protein At3g05340 OS=Arabidopsis thaliana GN=PCMP-E83 PE=2 SV=2

 Score =  135 bits (341), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 107/382 (28%), Positives = 168/382 (43%), Gaps = 66/382 (17%)

Query: 17  HAQLIS-TCLISSIFL-QLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKM--AL 72
           H  +I+ T +IS +   +L +D  R+F  +  R L   N++        C G+ ++    
Sbjct: 218 HRNVITLTAVISGLIENELHEDGLRLF-SLMRRGLVHPNSVTYLSALAACSGSQRIVEGQ 276

Query: 73  HLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMF 132
            +H L+ K+   S+  I  + +DM+ KCG+++ A              W         +F
Sbjct: 277 QIHALLWKYGIESELCIESALMDMYSKCGSIEDA--------------W--------TIF 314

Query: 133 QKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLE 192
           +   E D VS   ++  L ++G   E +  FI +   G  + + + +           L 
Sbjct: 315 ESTTEVDEVSMTVILVGLAQNGSEEEAIQFFIRMLQAGVEIDANVVSAVLGVSFIDNSLG 374

Query: 193 WGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKAD 252
            G  LHS V+  + S + FV +GLI+MY KCG                          + 
Sbjct: 375 LGKQLHSLVIKRKFSGNTFVNNGLINMYSKCG----------------------DLTDSQ 412

Query: 253 LAFELMSRRNMISWMVLISAFSQAG-------------VLEKPRFFFFFVSLLSGCSHSG 299
             F  M +RN +SW  +I+AF++ G              LE       F+SLL  CSH G
Sbjct: 413 TVFRRMPKRNYVSWNSMIAAFARHGHGLAALKLYEEMTTLEVKPTDVTFLSLLHACSHVG 472

Query: 300 PVTKGKHYFTAMAKF----TYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGAL 355
            + KG+     M +       T ++ C++D+LG +GLL EAK  ID +P KP C IW AL
Sbjct: 473 LIDKGRELLNEMKEVHGIEPRTEHYTCIIDMLGRAGLLKEAKSFIDSLPLKPDCKIWQAL 532

Query: 356 LGACCSHYNTKLAELVMRNLLQ 377
           LGAC  H +T++ E     L Q
Sbjct: 533 LGACSFHGDTEVGEYAAEQLFQ 554

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	385
297745590	789	unnamed protein product [Vitis vinifera]	0.685	0.334	0.426	8e-65
359491917	767	PREDICTED: pentatricopeptide repeat-cont	0.685	0.344	0.410	7e-62
255539304	742	pentatricopeptide repeat-containing prot	0.703	0.365	0.338	2e-48
147861799	1756	hypothetical protein VITISV_027167 [Viti	0.418	0.091	0.529	2e-44
449443642	663	PREDICTED: pentatricopeptide repeat-cont	0.776	0.450	0.319	3e-43
357438977	960	Pentatricopeptide repeat-containing prot	0.753	0.302	0.345	7e-43
356562443	836	PREDICTED: pentatricopeptide repeat-cont	0.789	0.363	0.295	1e-42
356562121	921	PREDICTED: pentatricopeptide repeat-cont	0.574	0.239	0.372	7e-42
294463969	514	unknown [Picea sitchensis]	0.805	0.603	0.304	8e-42
356532255	948	PREDICTED: pentatricopeptide repeat-cont	0.574	0.233	0.364	2e-40

>gi|297745590|emb|CBI40755.3| unnamed protein product [Vitis vinifera]

 Score =  253 bits (647), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 148/347 (42%), Positives = 190/347 (54%), Gaps = 83/347 (23%)

Query: 1   MKACGSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIGPRYL 49
           MK C SL+S+PIARK+HAQLI   L SSIFLQ           LI D YRVF  I    +
Sbjct: 11  MKECASLRSIPIARKLHAQLIFMGLKSSIFLQNHLLNMYSNCGLISDAYRVFGGIMFPNV 70

Query: 50  FTYNTMI------------------------------------NGGVRCL-----CVGNI 68
           +++NTMI                                    NG +         +G +
Sbjct: 71  YSWNTMISGFADSGQMREAEKLFEKMPERDSVSWNSMMSGYFHNGELEATIKASGSLGYL 130

Query: 69  KMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW------- 121
           K+AL LHG  +KF F  D  +  S +DM++KCGA+D+A+  F R  NPSLFCW       
Sbjct: 131 KLALQLHGFAEKFDFGIDTCVETSVLDMYIKCGAMDFAQKVFCRTPNPSLFCWNSMIYGY 190

Query: 122 -KFGIIR-LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYA 179
            K+G ++  L +F KMPERD VSWNTMISIL++HGFG ETL TF+E+WN GF  +SM YA
Sbjct: 191 SKYGSVKKALELFAKMPERDTVSWNTMISILSQHGFGAETLNTFLEMWNQGFRPNSMTYA 250

Query: 180 TAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALV 239
           +  SA  S+YDLEWG HLH+R+V MEP LDV+ G GLIDMY KCG   +ES+ Q+     
Sbjct: 251 SVLSACTSIYDLEWGAHLHARIVRMEPCLDVYAGCGLIDMYAKCG--RLESARQV----- 303

Query: 240 TMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF 286
                          F+ ++  N +SW  LI   +QAG  E+    F
Sbjct: 304 ---------------FDGLTEHNAVSWTSLIGGVAQAGFQEEALVLF 335

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359491917|ref|XP_003634341.1| PREDICTED: pentatricopeptide repeat-containing protein At2g13600-like [Vitis vinifera]

 Score =  244 bits (622), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 152/370 (41%), Positives = 193/370 (52%), Gaps = 106/370 (28%)

Query: 1   MKACGSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVF-------- 41
           MK C SL+S+PIARK+HAQLI   L SSIFLQ           LI D YRVF        
Sbjct: 1   MKECASLRSIPIARKLHAQLIFMGLKSSIFLQNHLLNMYSNCGLISDAYRVFGGIMFPNV 60

Query: 42  ----------CDIG-------------PRYLFTYNTMING----------------GVR- 61
                      D G              R   ++N+M++G                 VR 
Sbjct: 61  YSWNTMISGFADSGQMREAEKLFEKMPERDSVSWNSMMSGYFHNGELEATIKVFVSMVRD 120

Query: 62  CLCV----------------GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDY 105
           C CV                G +K+AL LHG  +KF F  D  +  S +DM++KCGA+D+
Sbjct: 121 CCCVPDPFSFSCVMKASGSLGYLKLALQLHGFAEKFDFGIDTCVETSVLDMYIKCGAMDF 180

Query: 106 AESAFLRMLNPSLFCW--------KFGIIR-LLIMFQKMPERDLVSWNTMISILTRHGFG 156
           A+  F R  NPSLFCW        K+G ++  L +F KMPERD VSWNTMISIL++HGFG
Sbjct: 181 AQKVFCRTPNPSLFCWNSMIYGYSKYGSVKKALELFAKMPERDTVSWNTMISILSQHGFG 240

Query: 157 FETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL 216
            ETL TF+E+WN GF  +SM YA+  SA  S+YDLEWG HLH+R+V MEP LDV+ G GL
Sbjct: 241 AETLNTFLEMWNQGFRPNSMTYASVLSACTSIYDLEWGAHLHARIVRMEPCLDVYAGCGL 300

Query: 217 IDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQA 276
           IDMY KCG   +ES+ Q+                    F+ ++  N +SW  LI   +QA
Sbjct: 301 IDMYAKCG--RLESARQV--------------------FDGLTEHNAVSWTSLIGGVAQA 338

Query: 277 GVLEKPRFFF 286
           G  E+    F
Sbjct: 339 GFQEEALVLF 348

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539304|ref|XP_002510717.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223551418|gb|EEF52904.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 132/390 (33%), Positives = 182/390 (46%), Gaps = 119/390 (30%)

Query: 5   GSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIGPRYLFTY- 52
           G   S+PIARK+HAQLIST L  SIFL            L  D  RVF D+  R +F+Y 
Sbjct: 2   GHCSSMPIARKLHAQLISTGLYISIFLHNHLLNMYLNCHLTHDACRVFADMTFRNVFSYN 61

Query: 53  ------------------------------NTMINGGVR--------------------- 61
                                         N+M++G  R                     
Sbjct: 62  TMITGLSKAEQIDKAKKVFDEMPERDSVSWNSMMSGYFRNGKYEEVVKVFVLMIRNFTCI 121

Query: 62  ------------CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA 109
                       C  +G  K+A+ LHGL +KF F SD+SI  S + M++KCGA  YA+  
Sbjct: 122 VNLLSFSCAMKACGALGCFKLAIQLHGLFEKFDFGSDKSIETSVMGMYIKCGAFTYADRV 181

Query: 110 FLRMLNPSLFCWK---------FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETL 160
           FL +  PSLFC+          +G+ + L +F ++PERD VSW+T+ISIL+RHGFG  TL
Sbjct: 182 FLGIRQPSLFCFNSMLYCYSNSYGVGKALDLFNRIPERDSVSWSTIISILSRHGFGVPTL 241

Query: 161 CTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY 220
             FIE+W  GF  +SM +A   SA  S++DLEWG HLH+R++  E  LD +VG+GL+ MY
Sbjct: 242 SMFIEMWTQGFRPNSMTFACVLSACTSIHDLEWGAHLHARIIRKEIILDDYVGNGLVYMY 301

Query: 221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLE 280
            KC                      G  + A   F  ++  N +SW  LI+  ++ G+ E
Sbjct: 302 AKC----------------------GHLKFARRVFNSLTEHNAVSWTSLINGVARCGLKE 339

Query: 281 KPRFF-------------FFFVSLLSGCSH 297
           +                 F F ++L  CSH
Sbjct: 340 EALLLFNKMREVLVALDEFTFATVLKVCSH 369

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147861799|emb|CAN81086.1| hypothetical protein VITISV_027167 [Vitis vinifera]

 Score =  186 bits (471), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 91/172 (52%), Positives = 118/172 (68%), Gaps = 11/172 (6%)

Query: 77   LVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW--------KFG-IIR 127
            ++KKF F  D  +  S +DM++KCGA+D+A+  F R  NPSLFCW        K+G + +
Sbjct: 1542 VLKKFDFGIDTCVETSVLDMYIKCGAMDFAQKVFCRTSNPSLFCWNSMIYGYSKYGSVKK 1601

Query: 128  LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS 187
             L +F KMPERD VSWNTMISIL++HGFG ETL  F+E+W  GF  +SM YA+  SA  +
Sbjct: 1602 ALELFAKMPERDTVSWNTMISILSQHGFGAETLNMFLEMWKQGFRPNSMTYASVLSACTN 1661

Query: 188  VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALV 239
            +YDLEWG HLH+R+V MEP LDV+   GLIDMY KCG   +ES+ Q+   L 
Sbjct: 1662 IYDLEWGAHLHARIVRMEPRLDVYARCGLIDMYAKCG--RLESARQVFDGLT 1711

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443642|ref|XP_004139586.1| PREDICTED: pentatricopeptide repeat-containing protein At2g13600-like [Cucumis sativus] gi|449492832|ref|XP_004159115.1| PREDICTED: pentatricopeptide repeat-containing protein At2g13600-like [Cucumis sativus]

 Score =  182 bits (462), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 122/382 (31%), Positives = 183/382 (47%), Gaps = 83/382 (21%)

Query: 62  CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW 121
           C  VG I++A  LHGL +K+ F +++ I  S IDM++KC A+  AE  FLR+  PSLF W
Sbjct: 3   CSSVGYIRIAHQLHGLSEKYGFGNNKVIQNSIIDMYIKCDAIYAAEQVFLRIEKPSLFSW 62

Query: 122 K---FGIIRLLIM------FQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFG 172
               +G  +L  M      F++MPERD VSWNT+IS  + HG   ++L TF+E+W  G  
Sbjct: 63  NCMIYGYSKLHEMGRAIDTFRQMPERDSVSWNTIISAFSHHGLHIQSLGTFVEMWIQGCQ 122

Query: 173 LSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSI 232
            +SM YA+  SA A++YD +WG HLH+R+V +EP LDV VG+GL+DMY KCG   I++S 
Sbjct: 123 PNSMTYASVLSACANIYDFQWGKHLHARIVRVEPFLDVLVGNGLVDMYAKCGL--IDASK 180

Query: 233 QIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFF----- 287
           ++                    F  +   N+++W  LIS  +  G  E+    F+     
Sbjct: 181 RV--------------------FNTLREHNVVTWTSLISGIAHFGSQEEVYDIFYQMRKD 220

Query: 288 --------FVSLLSGCSHSGPVTKGK--HYFTA---------MAKFTYTCYFVC------ 322
                     ++L  C     ++ G+  H FT          +   T + Y  C      
Sbjct: 221 CVIMDNFILATILGVCEGETNISIGEQLHGFTVKTGMNSSVPVGNATLSMYAKCGDFEKA 280

Query: 323 -----------------MVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSH--- 362
                            M+     SG +  A+   + MP +   + W A+LGA C +   
Sbjct: 281 SLAFETMAAHDVISWTTMITSFSHSGNVERARDYFNRMPER-NVISWNAMLGAYCQNSFW 339

Query: 363 -YNTKLAELVMRNLLQLDVKVF 383
               KL  L++R  ++ D   F
Sbjct: 340 EEGLKLYILMLRQEVRPDWITF 361

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357438977|ref|XP_003589765.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355478813|gb|AES60016.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  181 bits (458), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 115/333 (34%), Positives = 164/333 (49%), Gaps = 43/333 (12%)

Query: 62  CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW 121
           C  +G+ ++A+ LH LV K  F  +  I  S + M+VKCG VD AE+ F  +  PSLFCW
Sbjct: 156 CGSLGDSRLAIQLHALVSKLGFGMETCIQNSVVGMYVKCGDVDLAETVFFDIERPSLFCW 215

Query: 122 K---------FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFG 172
                     +G  + L +F +MPERD VSWNT+ISI ++HGFG + L  F+E+ N GF 
Sbjct: 216 NSMIYGYSQMYGPYKALQIFNRMPERDEVSWNTLISIFSQHGFGVQCLAMFVEMCNQGFS 275

Query: 173 LSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGC------- 225
            + M Y +  SA AS  DL+WG HLH+R++ ME SLD+  G+GLIDMY KCGC       
Sbjct: 276 PNFMTYGSVLSACASTSDLKWGAHLHARILRMEHSLDLVFGNGLIDMYAKCGCLDLAKRV 335

Query: 226 -NGIESSIQIG-KALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPR 283
              +     I   +L+T     G  + A + F  M R +++    ++      GV   P 
Sbjct: 336 FKSLREHDHISWNSLITGVVHFGLGEDALILFNQMRRSSVVLDEFILPTI--LGVCSGPD 393

Query: 284 F-----FFFFVSLLSGCSHSGPVTKGKHYFTAMAK---------------FTYTCYFVCM 323
           +          ++ SG   S PV  G    T  AK                  T  +  M
Sbjct: 394 YASTGELLHGYTIKSGMGSSAPV--GNAIITMYAKCGDTDKADLVFRLMPLRNTISWTAM 451

Query: 324 VDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALL 356
           +     SG +G+A+   D MP +   V W ++L
Sbjct: 452 ITAFSRSGDIGKARGYFDMMPER-NIVTWNSML 483

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562443|ref|XP_003549481.1| PREDICTED: pentatricopeptide repeat-containing protein At4g13650-like [Glycine max]

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 115/389 (29%), Positives = 172/389 (44%), Gaps = 85/389 (21%)

Query: 30  FLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESI 89
           F+ ++ D      +  P   F+Y   +     C C+ + + AL LH  V K +  +   I
Sbjct: 126 FMSMLRDSNHDIQNCDP---FSYTCTMKA---CGCLASTRFALQLHAHVIKLHLGAQTCI 179

Query: 90  AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK---------FGIIRLLIMFQKMPERDL 140
             S +DM++KCGA+  AE+ FL + +PSLFCW          +G    L +F +MPERD 
Sbjct: 180 QNSLVDMYIKCGAITLAETVFLNIESPSLFCWNSMIYGYSQLYGPYEALHVFTRMPERDH 239

Query: 141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSR 200
           VSWNT+IS+ +++G G   L TF+E+ N GF  + M Y +  SA AS+ DL+WG HLH+R
Sbjct: 240 VSWNTLISVFSQYGHGIRCLSTFVEMCNLGFKPNFMTYGSVLSACASISDLKWGAHLHAR 299

Query: 201 VVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR 260
           ++ ME SLD F+GSGLIDMY KCGC  +   +                      F  +  
Sbjct: 300 ILRMEHSLDAFLGSGLIDMYAKCGCLALARRV----------------------FNSLGE 337

Query: 261 RNMISWMVLISAFSQAGVLEKPRFF-------------FFFVSLLSGCS----------- 296
           +N +SW  LIS  +Q G+ +                  F   ++L  CS           
Sbjct: 338 QNQVSWTCLISGVAQFGLRDDALALFNQMRQASVVLDEFTLATILGVCSGQNYAATGELL 397

Query: 297 HSGPVTKGKHYFTAMAKFTYTCYFVC-----------------------MVDLLGLSGLL 333
           H   +  G   F  +     T Y  C                       M+     +G +
Sbjct: 398 HGYAIKSGMDSFVPVGNAIITMYARCGDTEKASLAFRSMPLRDTISWTAMITAFSQNGDI 457

Query: 334 GEAKKLIDEMPSKPTCVIWGALLGACCSH 362
             A++  D MP +   + W ++L     H
Sbjct: 458 DRARQCFDMMPER-NVITWNSMLSTYIQH 485

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562121|ref|XP_003549322.1| PREDICTED: pentatricopeptide repeat-containing protein At2g13600-like [Glycine max]

 Score =  177 bits (449), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 96/258 (37%), Positives = 139/258 (53%), Gaps = 37/258 (14%)

Query: 30  FLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESI 89
           F+ ++ D      +  P   F+Y   +     C C+ + ++AL LH  V K +  +   I
Sbjct: 126 FMSMLRDSNHDIQNCDP---FSYTCTMKA---CGCLASTRLALQLHAHVIKLHLGAQTCI 179

Query: 90  AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK---------FGIIRLLIMFQKMPERDL 140
             S +DM++KCGA+  AE+ FL + +PSLFCW          +G    L +F +MPERD 
Sbjct: 180 QNSLVDMYIKCGAITLAETIFLNIESPSLFCWNSMIYGYSQLYGPYEALHVFTRMPERDH 239

Query: 141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSR 200
           VSWNT+IS+ +++G G   L TF+E+ N GF  + M Y +  SA AS+ DL+WG HLH+R
Sbjct: 240 VSWNTLISVFSQYGHGIRCLSTFVEMCNLGFKPNFMTYGSVLSACASISDLKWGAHLHAR 299

Query: 201 VVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR 260
           ++ ME SLD F+GSGLIDMY KCGC  +                      A   F  +  
Sbjct: 300 ILRMEHSLDAFLGSGLIDMYAKCGCLAL----------------------ARRVFNSLGE 337

Query: 261 RNMISWMVLISAFSQAGV 278
           +N +SW   IS  +Q G+
Sbjct: 338 QNQVSWTCFISGVAQFGL 355

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294463969|gb|ADE77505.1| unknown [Picea sitchensis]

 Score =  177 bits (449), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 110/361 (30%), Positives = 175/361 (48%), Gaps = 51/361 (14%)

Query: 50  FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA 109
           FT +T++     C  + +++     H  + K  F SD  +  + + M+ +CG+++ A   
Sbjct: 11  FTLSTVVKA---CASIASLEQGKQAHNYIIKMGFESDVVVQTALVHMYARCGSLEDAGHV 67

Query: 110 FLRMLNPSLFCWKFGII---------RLLIMFQKMPERDLVSWNTMISILTRHGFGFETL 160
           F +M   S   W   I          + L +F +M ERD+VSW  +I+   ++G+G E+L
Sbjct: 68  FDKMSERSTRTWNAMITGHAQNRDMKKALKLFYEMSERDVVSWTAVIAGYAQNGYGDESL 127

Query: 161 CTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY 220
             F ++   G      +  +  SA A +  LE G   H+ VV    +LD+ VGS L+DM 
Sbjct: 128 NVFNQMRKTGMKSDRFIMGSVLSACADLAALELGRQFHAYVVQSGFALDIVVGSALVDM- 186

Query: 221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLE 280
                                YA+ GS + A   F+ M +RN +SW  +I+  +Q G   
Sbjct: 187 ---------------------YAKSGSMEDACQVFDKMPQRNEVSWNSIITGCAQHGRGN 225

Query: 281 KPRFFF-------------FFVSLLSGCSHSGPVTKGKHYFTAMAK----FTYTCYFVCM 323
                F              FV +LS CSH+G V +G+ YF  M +         ++ CM
Sbjct: 226 DAVLLFEQMLQAGIKPNEISFVGVLSACSHTGLVNEGRGYFNLMTQNYGIVPDVSHYTCM 285

Query: 324 VDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF 383
           +DLLG +G L EA+  I+ MP +P   +WGALLGAC  H NT+LA+ +  +LL ++V++ 
Sbjct: 286 IDLLGRAGCLDEAENFINGMPVEPDVSVWGALLGACRIHGNTELAKRIAEHLLGMEVQIA 345

Query: 384 G 384
           G
Sbjct: 346 G 346

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532255|ref|XP_003534689.1| PREDICTED: pentatricopeptide repeat-containing protein At4g33170-like [Glycine max]

 Score =  173 bits (438), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 94/258 (36%), Positives = 138/258 (53%), Gaps = 37/258 (14%)

Query: 30  FLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESI 89
           F+ ++ D      +  P   F+Y   +     C C+ + + AL LH  V K +  +   I
Sbjct: 126 FMSMLRDSNHDIQNCDP---FSYTCTMKA---CGCLASTRFALQLHAHVIKLHLGAQTCI 179

Query: 90  AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK---------FGIIRLLIMFQKMPERDL 140
             S +DM++KCGA+  AE+ FL + +PSLFCW          +G    L +F +MP+ D 
Sbjct: 180 QNSLVDMYIKCGAITLAETVFLNIESPSLFCWNSMIYGYSQLYGPYEALHVFTRMPKHDH 239

Query: 141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSR 200
           VSWNT+IS+ +++G G   L T++E+ N GF  + M Y +  SA AS+ DL+WG HLH+R
Sbjct: 240 VSWNTLISVFSQYGHGIRCLSTYVEMCNLGFKPNFMTYGSVLSACASISDLKWGAHLHAR 299

Query: 201 VVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR 260
           ++ ME SLD F+GSGLIDMY KCGC  +                      A   F  +  
Sbjct: 300 ILRMEHSLDAFLGSGLIDMYAKCGCLAL----------------------ARRVFNSLGE 337

Query: 261 RNMISWMVLISAFSQAGV 278
           +N +SW  LIS  +Q G+
Sbjct: 338 QNQVSWTCLISGVAQFGL 355

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	385
TAIR|locus:2054131	697	SLO2 "AT2G13600" [Arabidopsis	0.802	0.443	0.316	2e-36
TAIR|locus:2140235	781	AT4G02750 [Arabidopsis thalian	0.618	0.304	0.349	2e-32
TAIR|locus:2154855	620	AT5G66520 "AT5G66520" [Arabido	0.851	0.529	0.295	2.1e-32
TAIR|locus:2196583	866	ECB2 "EARLY CHLOROPLAST BIOGEN	0.641	0.285	0.316	6.8e-31
TAIR|locus:2045580	559	AT2G42920 [Arabidopsis thalian	0.779	0.536	0.317	1.4e-30
TAIR|locus:2095487	504	AT3G28660 "AT3G28660" [Arabido	0.597	0.456	0.316	2.7e-29
TAIR|locus:2150936	623	AT5G15340 [Arabidopsis thalian	0.771	0.476	0.301	6.9e-29
TAIR|locus:2154389	646	LPA66 "LOW PSII ACCUMULATION 6	0.620	0.369	0.342	2.3e-28
TAIR|locus:2198678	500	PDE247 "pigment defective 247"	0.625	0.482	0.326	2.4e-28
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.919	0.477	0.282	3.8e-28

TAIR|locus:2054131 SLO2 "AT2G13600" [Arabidopsis thaliana (taxid:3702)]

 Score = 368 (134.6 bits), Expect = 2.0e-36, Sum P(2) = 2.0e-36
 Identities = 107/338 (31%), Positives = 165/338 (48%)

Query:    62 CLCVGNIKMALHLHG-LVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF----LR--ML 114
             C  +  IK+   +HG +VK     +D  ++ + +DM+ KC  +  A   F    +R  + 
Sbjct:   263 CASLSAIKVGQEVHGRVVKNDKLRNDIILSNAFVDMYAKCSRIKEARFIFDSMPIRNVIA 322

Query:   115 NPSL---FCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGF 171
               S+   +          +MF KM ER++VSWN +I+  T++G   E L  F  L     
Sbjct:   323 ETSMISGYAMAASTKAARLMFTKMAERNVVSWNALIAGYTQNGENEEALSLFCLLKRESV 382

Query:   172 GLSSMLYATAFSARASVYDLEWGPHLHSRVV-H-----MEPSLDVFVGSGLIDMYLKCGC 225
               +   +A    A A + +L  G   H  V+ H          D+FVG+ LIDMY+KCGC
Sbjct:   383 CPTHYSFANILKACADLAELHLGMQAHVHVLKHGFKFQSGEEDDIFVGNSLIDMYVKCGC 442

Query:   226 NGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFF 285
               +E    + + +  M  +  S     + F      N    + L     ++G  EKP   
Sbjct:   443 --VEEGYLVFRKM--MERDCVSWNAMIIGFAQNGYGNEA--LELFREMLESG--EKPDHI 494

Query:   286 FFFVSLLSGCSHSGPVTKGKHYFTAMAK-FTYTC---YFVCMVDLLGLSGLLGEAKKLID 341
                + +LS C H+G V +G+HYF++M + F       ++ CMVDLLG +G L EAK +I+
Sbjct:   495 TM-IGVLSACGHAGFVEEGRHYFSSMTRDFGVAPLRDHYTCMVDLLGRAGFLEEAKSMIE 553

Query:   342 EMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLD 379
             EMP +P  VIWG+LL AC  H N  L + V   LL+++
Sbjct:   554 EMPMQPDSVIWGSLLAACKVHRNITLGKYVAEKLLEVE 591

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0010182 "sugar mediated signaling pathway" evidence=IMP

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2140235 AT4G02750 [Arabidopsis thaliana (taxid:3702)]

 Score = 330 (121.2 bits), Expect = 2.0e-32, Sum P(2) = 2.0e-32
 Identities = 89/255 (34%), Positives = 130/255 (50%)

Query:   131 MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYD 190
             +F KMP+RD VSW  MI+  ++ G  FE L  F+++   G  L+   +++A S  A V  
Sbjct:   365 LFDKMPKRDPVSWAAMIAGYSQSGHSFEALRLFVQMEREGGRLNRSSFSSALSTCADVVA 424

Query:   191 LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQK 250
             LE G  LH R+V        FVG+ L+ MY KCG   IE +  + K +        +T  
Sbjct:   425 LELGKQLHGRLVKGGYETGCFVGNALLLMYCKCG--SIEEANDLFKEMAGKDIVSWNTMI 482

Query:   251 ADLAFELMSRRNMISWMVL--ISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYF 308
             A  +      R+    + L    +  + G+  KP      V++LS CSH+G V KG+ YF
Sbjct:   483 AGYS------RHGFGEVALRFFESMKREGL--KPDDATM-VAVLSACSHTGLVDKGRQYF 533

Query:   309 TAMAK----FTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYN 364
               M +       + ++ CMVDLLG +GLL +A  L+  MP +P   IWG LLGA   H N
Sbjct:   534 YTMTQDYGVMPNSQHYACMVDLLGRAGLLEDAHNLMKNMPFEPDAAIWGTLLGASRVHGN 593

Query:   365 TKLAELVMRNLLQLD 379
             T+LAE     +  ++
Sbjct:   594 TELAETAADKIFAME 608

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2154855 AT5G66520 "AT5G66520" [Arabidopsis thaliana (taxid:3702)]

 Score = 360 (131.8 bits), Expect = 2.1e-32, P = 2.1e-32
 Identities = 105/355 (29%), Positives = 168/355 (47%)

Query:    39 RVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHV 98
             R+ C   P   +T+ +++     C  +   +    +H  + K  + +D     S I+ + 
Sbjct:   105 RMLCSSAPHNAYTFPSLLKA---CSNLSAFEETTQIHAQITKLGYENDVYAVNSLINSYA 161

Query:    99 KCGAVDYAESAFLRMLNPSLFCWKF---GIIRL------LIMFQKMPERDLVSWNTMISI 149
               G    A   F R+  P    W     G ++       L +F+KM E++ +SW TMIS 
Sbjct:   162 VTGNFKLAHLLFDRIPEPDDVSWNSVIKGYVKAGKMDIALTLFRKMAEKNAISWTTMISG 221

Query:   150 LTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLD 209
               +     E L  F E+ N      ++  A A SA A +  LE G  +HS +      +D
Sbjct:   222 YVQADMNKEALQLFHEMQNSDVEPDNVSLANALSACAQLGALEQGKWIHSYLNKTRIRMD 281

Query:   210 VFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVL 269
               +G  LIDMY KCG   +E ++++ K +     +  +   +  A+    R  +  +M +
Sbjct:   282 SVLGCVLIDMYAKCG--EMEEALEVFKNIKKKSVQAWTALISGYAYHGHGREAISKFMEM 339

Query:   270 ISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTC-----YFVCMV 324
                  + G+  KP    F  ++L+ CS++G V +GK  F +M +  Y       ++ C+V
Sbjct:   340 ----QKMGI--KPNVITF-TAVLTACSYTGLVEEGKLIFYSMER-DYNLKPTIEHYGCIV 391

Query:   325 DLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLD 379
             DLLG +GLL EAK+ I EMP KP  VIWGALL AC  H N +L E +   L+ +D
Sbjct:   392 DLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRIHKNIELGEEIGEILIAID 446

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:2196583 ECB2 "EARLY CHLOROPLAST BIOGENESIS2" [Arabidopsis thaliana (taxid:3702)]

 Score = 283 (104.7 bits), Expect = 6.8e-31, Sum P(3) = 6.8e-31
 Identities = 84/265 (31%), Positives = 131/265 (49%)

Query:   125 IIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSA 184
             I + L +F  +P ++++SW ++I+ L  +   FE L  F+         +++    A +A
Sbjct:   449 IDKALDIFHNIPRKNVISWTSIIAGLRLNNRCFEALI-FLRQMKMTLQPNAITLTAALAA 507

Query:   185 RASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG-CNGIESSIQIGKALVTMYA 243
              A +  L  G  +H+ V+     LD F+ + L+DMY++CG  N   S     K  VT + 
Sbjct:   508 CARIGALMCGKEIHAHVLRTGVGLDDFLPNALLDMYVRCGRMNTAWSQFNSQKKDVTSW- 566

Query:   244 EGGSTQKADLAFELMSRRNMISWMV-LISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVT 302
                     ++     S R   S +V L     ++ V  +P    F +SLL GCS S  V 
Sbjct:   567 --------NILLTGYSERGQGSMVVELFDRMVKSRV--RPDEITF-ISLLCGCSKSQMVR 615

Query:   303 KGKHYFTAMAKFTYTC---YFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGAC 359
             +G  YF+ M  +  T    ++ C+VDLLG +G L EA K I +MP  P   +WGALL AC
Sbjct:   616 QGLMYFSKMEDYGVTPNLKHYACVVDLLGRAGELQEAHKFIQKMPVTPDPAVWGALLNAC 675

Query:   360 CSHYNTKLAELVMRNLLQLDVKVFG 384
               H+   L EL  +++ +LD K  G
Sbjct:   676 RIHHKIDLGELSAQHIFELDKKSVG 700

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

GO:0040007 "growth" evidence=IMP

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

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

 Score = 312 (114.9 bits), Expect = 1.4e-30, Sum P(2) = 1.4e-30
 Identities = 106/334 (31%), Positives = 158/334 (47%)

Query:    65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW--- 121
             +G  +    LHG+V K     D  I  + + M+V CG +  A   FL M+   +  W   
Sbjct:   139 LGQARDGRQLHGMVIKEGLEDDSFIRNTMLHMYVTCGCLIEAWRIFLGMIGFDVVAWNSM 198

Query:   122 -----KFGII-RLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH-----G 170
                  K G+I +   +F +MP+R+ VSWN+MIS   R+G   + L  F E+        G
Sbjct:   199 IMGFAKCGLIDQAQNLFDEMPQRNGVSWNSMISGFVRNGRFKDALDMFREMQEKDVKPDG 258

Query:   171 FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIES 230
             F + S+L A A+   AS    E G  +H  +V     L+  V + LIDMY KCGC  IE 
Sbjct:   259 FTMVSLLNACAYLG-AS----EQGRWIHEYIVRNRFELNSIVVTALIDMYCKCGC--IEE 311

Query:   231 SIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVS 290
              + + +          ++    LA      R M     L S   ++G LE     F  + 
Sbjct:   312 GLNVFECAPKKQLSCWNSMILGLANNGFEERAMD----LFSELERSG-LEPDSVSF--IG 364

Query:   291 LLSGCSHSGPVTKGKHYFTAMAKFTYTC-----YFVCMVDLLGLSGLLGEAKKLIDEMPS 345
             +L+ C+HSG V +   +F  M K  Y       ++  MV++LG +GLL EA+ LI  MP 
Sbjct:   365 VLTACAHSGEVHRADEFFRLM-KEKYMIEPSIKHYTLMVNVLGGAGLLEEAEALIKNMPV 423

Query:   346 KPTCVIWGALLGACCSHYNTKLAELVMRNLLQLD 379
             +   VIW +LL AC    N ++A+   + L +LD
Sbjct:   424 EEDTVIWSSLLSACRKIGNVEMAKRAAKCLKKLD 457

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2095487 AT3G28660 "AT3G28660" [Arabidopsis thaliana (taxid:3702)]

 Score = 290 (107.1 bits), Expect = 2.7e-29, Sum P(2) = 2.7e-29
 Identities = 84/265 (31%), Positives = 133/265 (50%)

Query:   131 MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYD 190
             +F ++P+ D+V W+ +++   R G G E L  F E+   G         TA +A A V  
Sbjct:   174 VFDEIPQPDVVKWDVLMNGYVRCGLGSEGLEVFKEMLVRGIEPDEFSVTTALTACAQVGA 233

Query:   191 LEWGPHLHSRVVHME-PSLDVFVGSGLIDMYLKCGCNGIESSIQIGK-----------AL 238
             L  G  +H  V        DVFVG+ L+DMY KCGC  IE+++++ +           AL
Sbjct:   234 LAQGKWIHEFVKKKRWIESDVFVGTALVDMYAKCGC--IETAVEVFEKLTRRNVFSWAAL 291

Query:   239 VTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHS 298
             +  YA  G  +KA    + + R +              G+  KP      + +L+ C+H 
Sbjct:   292 IGGYAAYGYAKKATTCLDRIERED--------------GI--KPDSVVL-LGVLAACAHG 334

Query:   299 GPVTKGKHYFTAM-AKFTYTC---YFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGA 354
             G + +G+     M A++  T    ++ C+VDL+  +G L +A  LI++MP KP   +WGA
Sbjct:   335 GFLEEGRTMLENMEARYGITPKHEHYSCIVDLMCRAGRLDDALDLIEKMPMKPLASVWGA 394

Query:   355 LLGACCSHYNTKLAELVMRNLLQLD 379
             LL  C +H N +L EL ++NLL L+
Sbjct:   395 LLNGCRTHKNVELGELAVQNLLDLE 419

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2150936 AT5G15340 [Arabidopsis thaliana (taxid:3702)]

 Score = 328 (120.5 bits), Expect = 6.9e-29, P = 6.9e-29
 Identities = 106/352 (30%), Positives = 169/352 (48%)

Query:    59 GVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL 118
             GV C  + ++  A   HG+  K   ++   +  + +DM+ KCG V   +  F  +   S+
Sbjct:   119 GV-CAKLEDLGFAQQGHGVAVKMGVLTSVKVCNALMDMYGKCGLVSEVKRIFEELEEKSV 177

Query:   119 FCW--------KF-GIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL-WN 168
               W        K+ G+ R   +F +MPER+ V+W  M++     GF  E L    E+ + 
Sbjct:   178 VSWTVVLDTVVKWEGLERGREVFHEMPERNAVAWTVMVAGYLGAGFTREVLELLAEMVFR 237

Query:   169 HGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL-------DVFVGSGLIDMYL 221
              G GL+ +   +  SA A   +L  G  +H   +  E  +       DV VG+ L+DMY 
Sbjct:   238 CGHGLNFVTLCSMLSACAQSGNLVVGRWVHVYALKKEMMMGEEASYDDVMVGTALVDMYA 297

Query:   222 KCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAG---- 277
             KCG   I+SS+ +                    F LM +RN+++W  L S  +  G    
Sbjct:   298 KCG--NIDSSMNV--------------------FRLMRKRNVVTWNALFSGLAMHGKGRM 335

Query:   278 VLEK-PRFF-------FFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY---TCYFVCMVDL 326
             V++  P+           F ++LS CSHSG V +G   F ++  +       ++ CMVDL
Sbjct:   336 VIDMFPQMIREVKPDDLTFTAVLSACSHSGIVDEGWRCFHSLRFYGLEPKVDHYACMVDL 395

Query:   327 LGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQL 378
             LG +GL+ EA+ L+ EMP  P  V+ G+LLG+C  H   ++AE + R L+Q+
Sbjct:   396 LGRAGLIEEAEILMREMPVPPNEVVLGSLLGSCSVHGKVEIAERIKRELIQM 447

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 291 (107.5 bits), Expect = 2.3e-28, Sum P(2) = 2.3e-28
 Identities = 87/254 (34%), Positives = 127/254 (50%)

Query:   130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY 189
             ++F KM +R +VSWNTMIS  + +GF  + +  F E+       + +   +   A + + 
Sbjct:   229 MLFDKMRQRSVVSWNTMISGYSLNGFFKDAVEVFREMKKGDIRPNYVTLVSVLPAISRLG 288

Query:   190 DLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQ 249
              LE G  LH         +D  +GS LIDMY KCG   IE +I + + L     E   T 
Sbjct:   289 SLELGEWLHLYAEDSGIRIDDVLGSALIDMYSKCGI--IEKAIHVFERLPR---ENVITW 343

Query:   250 KADL-AFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYF 308
              A +  F +  +      +       QAGV  +P    + ++LL+ CSH G V +G+ YF
Sbjct:   344 SAMINGFAIHGQAG--DAIDCFCKMRQAGV--RPSDVAY-INLLTACSHGGLVEEGRRYF 398

Query:   309 TAMAKFT----YTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYN 364
             + M           ++ CMVDLLG SGLL EA++ I  MP KP  VIW ALLGAC    N
Sbjct:   399 SQMVSVDGLEPRIEHYGCMVDLLGRSGLLDEAEEFILNMPIKPDDVIWKALLGACRMQGN 458

Query:   365 TKLAELVMRNLLQL 378
              ++ + V   L+ +
Sbjct:   459 VEMGKRVANILMDM 472

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0007020 "microtubule nucleation" evidence=RCA

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

 Score = 287 (106.1 bits), Expect = 2.4e-28, Sum P(2) = 2.4e-28
 Identities = 84/257 (32%), Positives = 125/257 (48%)

Query:   131 MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYD 190
             MF KMPERDL+SW  MI+   + G+  E L  F E+   G     +    A +A  ++  
Sbjct:   162 MFDKMPERDLISWTAMINGFVKKGYQEEALLWFREMQISGVKPDYVAIIAALNACTNLGA 221

Query:   191 LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQK 250
             L +G  +H  V+  +   +V V + LID+Y +CGC  +E + Q+   +        ++  
Sbjct:   222 LSFGLWVHRYVLSQDFKNNVRVSNSLIDLYCRCGC--VEFARQVFYNMEKRTVVSWNSVI 279

Query:   251 ADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTA 310
                A    +  N    +V      + G   KP    F    L+ CSH G V +G  YF  
Sbjct:   280 VGFA----ANGNAHESLVYFRKMQEKGF--KPDAVTF-TGALTACSHVGLVEEGLRYFQI 332

Query:   311 MAKFTYTC-----YFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNT 365
             M K  Y       ++ C+VDL   +G L +A KL+  MP KP  V+ G+LL AC +H N 
Sbjct:   333 M-KCDYRISPRIEHYGCLVDLYSRAGRLEDALKLVQSMPMKPNEVVIGSLLAACSNHGNN 391

Query:   366 -KLAELVMRNLLQLDVK 381
               LAE +M++L  L+VK
Sbjct:   392 IVLAERLMKHLTDLNVK 408

GO:0005739 "mitochondrion" evidence=ISM

GO:0009451 "RNA modification" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

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

 Score = 306 (112.8 bits), Expect = 3.8e-28, Sum P(2) = 3.8e-28
 Identities = 111/393 (28%), Positives = 188/393 (47%)

Query:    17 HAQLIS-TCLISSIFLQ-LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHL 74
             H  ++S T LI     +  I++  ++F +I  + + ++N MI+G       GN K AL L
Sbjct:   197 HRDVVSYTALIKGYASRGYIENAQKLFDEIPVKDVVSWNAMISGYAE---TGNYKEALEL 253

Query:    75 HGLVKKFYFVSDESIAKSSIDMHVKCGAV-----------DYAESAFLRMLNPSLFCW-K 122
                + K     DES   + +    + G++           D+   + L+++N  +  + K
Sbjct:   254 FKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQVHLWIDDHGFGSNLKIVNALIDLYSK 313

Query:   123 FGIIRLLI-MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATA 181
              G +     +F+++P +D++SWNT+I   T      E L  F E+   G   + +   + 
Sbjct:   314 CGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSI 373

Query:   182 FSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSG-----LIDMYLKCGCNGIESSIQIGK 236
               A A +  ++ G  +H   V+++  L     +      LIDMY KCG   IE++ Q+  
Sbjct:   374 LPACAHLGAIDIGRWIH---VYIDKRLKGVTNASSLRTSLIDMYAKCG--DIEAAHQVFN 428

Query:   237 ALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCS 296
             ++  ++    S       F +  R +  +   L S   + G+  +P    F V LLS CS
Sbjct:   429 SI--LHKSLSSWNAMIFGFAMHGRAD--ASFDLFSRMRKIGI--QPDDITF-VGLLSACS 481

Query:   297 HSGPVTKGKHYFTAMA---KFTYTC-YFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIW 352
             HSG +  G+H F  M    K T    ++ CM+DLLG SGL  EA+++I+ M  +P  VIW
Sbjct:   482 HSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKEAEEMINMMEMEPDGVIW 541

Query:   353 GALLGACCSHYNTKLAELVMRNLLQLDVKVFGS 385
              +LL AC  H N +L E    NL++++ +  GS
Sbjct:   542 CSLLKACKMHGNVELGESFAENLIKIEPENPGS 574

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	385
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-39
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	9e-38
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-17
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-16
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-14
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-13
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	0.001

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

 Score =  148 bits (376), Expect = 3e-39
 Identities = 106/442 (23%), Positives = 186/442 (42%), Gaps = 106/442 (23%)

Query: 3   ACGSLKSLPIARKIHAQLISTCLISSI-----FLQL------IDDDYRVFCDIGPRYLFT 51
           AC  L    + R++H  ++ T     +      +Q+        +  +VF  +  +   +
Sbjct: 297 ACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVS 356

Query: 52  YNTMINGGVR--------------------------------CLCVGNIKMALHLHGLVK 79
           +  MI+G  +                                C C+G++ + + LH L +
Sbjct: 357 WTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAE 416

Query: 80  KFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD 139
           +   +S   +A + I+M+ KC  +D A                      L +F  +PE+D
Sbjct: 417 RKGLISYVVVANALIEMYSKCKCIDKA----------------------LEVFHNIPEKD 454

Query: 140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHS 199
           ++SW ++I+ L  +   FE L  F ++       +S+    A SA A +  L  G  +H+
Sbjct: 455 VISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGALMCGKEIHA 513

Query: 200 RVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMS 259
            V+      D F+ + L+D+Y++CG        ++  A         ++ + D+      
Sbjct: 514 HVLRTGIGFDGFLPNALLDLYVRCG--------RMNYAWNQF-----NSHEKDVV----- 555

Query: 260 RRNMISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKH 306
                SW +L++ +   G        F              F+SLL  CS SG VT+G  
Sbjct: 556 -----SWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLE 610

Query: 307 YFTAM-AKFTYTC---YFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSH 362
           YF +M  K++ T    ++ C+VDLLG +G L EA   I++MP  P   +WGALL AC  H
Sbjct: 611 YFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIH 670

Query: 363 YNTKLAELVMRNLLQLDVKVFG 384
            + +L EL  +++ +LD    G
Sbjct: 671 RHVELGELAAQHIFELDPNSVG 692

Length = 857

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

 Score =  143 bits (363), Expect = 9e-38
 Identities = 109/434 (25%), Positives = 175/434 (40%), Gaps = 104/434 (23%)

Query: 3   ACGSLKSLPIARKIHAQLIST-----------CLISSIFLQLIDDDYRVFCDIGPRYLFT 51
           AC +LKS+   + ++  + S+            L+  +   ++ D  R+F ++  R L +
Sbjct: 132 ACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLAS 191

Query: 52  YNTMINGGV------------------------RCLCV--------GNIKMALHLHGLVK 79
           + T+I G V                        R   V        G+ +    LH  V 
Sbjct: 192 WGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVL 251

Query: 80  KFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD 139
           K   V D  ++ + IDM+ KCG ++ A   F                        MPE+ 
Sbjct: 252 KTGVVGDTFVSCALIDMYSKCGDIEDARCVF----------------------DGMPEKT 289

Query: 140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHS 199
            V+WN+M++    HG+  E LC + E+ + G  +    ++      + +  LE     H+
Sbjct: 290 TVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLE-----HA 344

Query: 200 RVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMS 259
           +  H          +GLI         G    I    ALV +Y++ G  + A   F+ M 
Sbjct: 345 KQAH----------AGLIR-------TGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP 387

Query: 260 RRNMISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKH 306
           R+N+ISW  LI+ +   G   K    F              F+++LS C +SG   +G  
Sbjct: 388 RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWE 447

Query: 307 YFTAMAKFTYT----CYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSH 362
            F +M++         ++ CM++LLG  GLL EA  +I   P KPT  +W ALL AC  H
Sbjct: 448 IFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIH 507

Query: 363 YNTKLAELVMRNLL 376
            N +L  L    L 
Sbjct: 508 KNLELGRLAAEKLY 521

Length = 697

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

 Score = 82.6 bits (204), Expect = 4e-17
 Identities = 72/328 (21%), Positives = 118/328 (35%), Gaps = 64/328 (19%)

Query: 51  TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF 110
           TY+ ++     C+ + +I+    ++  V+   F  D+ +    + MHVKCG +  A   F
Sbjct: 125 TYDALVEA---CIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLF 181

Query: 111 LRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHG 170
                                  +MPER+L SW T+I  L   G   E    F E+W  G
Sbjct: 182 ----------------------DEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDG 219

Query: 171 FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIES 230
                  +     A A +     G  LH  V+      D FV   LIDMY KC       
Sbjct: 220 SDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKC------- 272

Query: 231 SIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFF----- 285
                          G  + A   F+ M  +  ++W  +++ ++  G  E+         
Sbjct: 273 ---------------GDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMR 317

Query: 286 --------FFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFV---CMVDLLGLSGLLG 334
                   F F  ++   S    +   K     + +  +    V    +VDL    G + 
Sbjct: 318 DSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRME 377

Query: 335 EAKKLIDEMPSKPTCVIWGALLGACCSH 362
           +A+ + D MP K   + W AL+    +H
Sbjct: 378 DARNVFDRMPRK-NLISWNALIAGYGNH 404

Length = 697

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

 Score = 81.4 bits (201), Expect = 1e-16
 Identities = 60/264 (22%), Positives = 101/264 (38%), Gaps = 56/264 (21%)

Query: 54  TMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRM 113
           T+ +    C  +G+ ++   +HG V K  F  D S+  S I M++  G+   AE      
Sbjct: 290 TITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEK----- 344

Query: 114 LNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL 173
                            +F +M  +D VSW  MIS   ++G   + L T+  +       
Sbjct: 345 -----------------VFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSP 387

Query: 174 SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQ 233
             +  A+  SA A + DL+ G  LH           V V + LI+MY KC C  I+ +++
Sbjct: 388 DEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKC--IDKALE 445

Query: 234 IGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF------- 286
           +                    F  +  +++ISW  +I+         +   FF       
Sbjct: 446 V--------------------FHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTL 485

Query: 287 -----FFVSLLSGCSHSGPVTKGK 305
                  ++ LS C+  G +  GK
Sbjct: 486 KPNSVTLIAALSACARIGALMCGK 509

Length = 857

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

 Score = 74.9 bits (184), Expect = 2e-14
 Identities = 67/278 (24%), Positives = 103/278 (37%), Gaps = 76/278 (27%)

Query: 36  DDYRVFCDIGPRYLFTYNTMING--------------------GVR------------CL 63
             + VF  +  R LF++N ++ G                    GVR            C 
Sbjct: 139 HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCG 198

Query: 64  CVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKF 123
            + ++     +H  V +F F  D  +  + I M+VKCG V  A     R++         
Sbjct: 199 GIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSA-----RLV--------- 244

Query: 124 GIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS 183
                   F +MP RD +SWN MIS    +G   E L  F  +         M   +  S
Sbjct: 245 --------FDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVIS 296

Query: 184 ARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA 243
           A   + D   G  +H  VV    ++DV V + LI MYL  G  G                
Sbjct: 297 ACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWG---------------- 340

Query: 244 EGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEK 281
                 +A+  F  M  ++ +SW  +IS + + G+ +K
Sbjct: 341 ------EAEKVFSRMETKDAVSWTAMISGYEKNGLPDK 372

Length = 857

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

 Score = 72.2 bits (177), Expect = 1e-13
 Identities = 75/272 (27%), Positives = 110/272 (40%), Gaps = 52/272 (19%)

Query: 108 SAFLRMLNPSLFCWKFG-IIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE- 165
           +A L M        +FG ++    +F KMPERDL SWN ++    + G+  E LC +   
Sbjct: 125 NAMLSMF------VRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRM 178

Query: 166 LWNHGFGLSSMLYATAFSAR--ASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC 223
           LW    G+   +Y      R    + DL  G  +H+ VV                     
Sbjct: 179 LW---AGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRF------------------- 216

Query: 224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGV-LEKP 282
              G E  + +  AL+TMY + G    A L F+ M RR+ ISW  +IS + + G  LE  
Sbjct: 217 ---GFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGL 273

Query: 283 RFFF----FFV--------SLLSGCSHSGPVTKGK--HYFTAMAKFTYTCYFVCMVDLLG 328
             FF      V        S++S C   G    G+  H +     F         +  + 
Sbjct: 274 ELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMY 333

Query: 329 LS-GLLGEAKKLIDEMPSKPTCVIWGALLGAC 359
           LS G  GEA+K+   M +K   V W A++   
Sbjct: 334 LSLGSWGEAEKVFSRMETKDA-VSWTAMISGY 364

Length = 857

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

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 31/151 (20%), Positives = 61/151 (40%), Gaps = 35/151 (23%)

Query: 231 SIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLE---------- 280
            +++G A+++M+   G    A   F  M  R++ SW VL+  +++AG  +          
Sbjct: 120 GVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRML 179

Query: 281 ----KPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----------TCYFVCMVD 325
               +P   + F  +L  C     + +G+     + +F +           T Y  C   
Sbjct: 180 WAGVRPD-VYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKC--- 235

Query: 326 LLGLSGLLGEAKKLIDEMPSKPTCVIWGALL 356
                G +  A+ + D MP +  C+ W A++
Sbjct: 236 -----GDVVSARLVFDRMPRR-DCISWNAMI 260

Length = 857

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	385
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
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
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.93
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.92
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.88
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.82
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.81
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.79
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.78
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.76
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.74
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.72
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.72
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.71
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.71
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.7
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.66
PRK14574	822	hmsH outer membrane protein; Provisional	99.66
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.62
PRK14574	822	hmsH outer membrane protein; Provisional	99.61
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.59
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.55
PF13041	50	PPR_2: PPR repeat family	99.51
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.51
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.48
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.45
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.45
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.44
PF13041	50	PPR_2: PPR repeat family	99.42
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.42
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.41
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.41
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.38
KOG1126	638	consensus DNA-binding cell division cycle control	99.35
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.34
KOG2076	895	consensus RNA polymerase III transcription factor	99.32
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.3
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.29
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.26
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.22
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.21
KOG2076	895	consensus RNA polymerase III transcription factor	99.2
KOG2003	840	consensus TPR repeat-containing protein [General f	99.2
KOG1126	638	consensus DNA-binding cell division cycle control	99.2
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.2
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.2
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.17
KOG2003	840	consensus TPR repeat-containing protein [General f	99.15
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.14
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.12
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.11
PRK12370	553	invasion protein regulator; Provisional	99.09
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.09
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.07
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.07
PRK12370	553	invasion protein regulator; Provisional	99.06
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.04
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.04
KOG1129	478	consensus TPR repeat-containing protein [General f	99.04
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.94
PF12854	34	PPR_1: PPR repeat	98.94
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.91
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.87
PRK11189	296	lipoprotein NlpI; Provisional	98.85
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.85
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.83
KOG1129	478	consensus TPR repeat-containing protein [General f	98.81
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.79
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.75
PRK11189	296	lipoprotein NlpI; Provisional	98.75
PF12854	34	PPR_1: PPR repeat	98.68
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.68
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.66
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.65
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.64
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.62
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.61
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.61
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.6
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.58
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.52
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.52
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.52
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.49
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.47
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.46
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.46
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.44
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.43
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.42
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.42
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.38
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.38
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.31
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.3
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.29
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.27
PRK04841	903	transcriptional regulator MalT; Provisional	98.27
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.27
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.25
KOG1125	579	consensus TPR repeat-containing protein [General f	98.24
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.22
PRK15359	144	type III secretion system chaperone protein SscB;	98.21
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.18
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.18
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.18
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.16
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	98.13
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.12
PRK04841	903	transcriptional regulator MalT; Provisional	98.11
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.1
PLN02789	320	farnesyltranstransferase	98.09
PLN02789	320	farnesyltranstransferase	98.07
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.06
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.05
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.04
PRK15359	144	type III secretion system chaperone protein SscB;	98.04
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.01
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.01
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.0
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.0
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.0
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.0
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.99
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.99
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.98
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.97
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	97.96
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.95
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.95
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.95
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.93
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.9
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.9
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.89
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.79
KOG1125	579	consensus TPR repeat-containing protein [General f	97.77
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.76
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.76
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.76
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.73
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.71
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.68
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	97.68
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.64
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.6
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.57
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.56
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	97.54
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.53
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.51
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.5
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.47
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.42
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.41
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.41
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.4
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.39
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.38
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.35
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.35
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.35
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.3
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.3
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.22
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.17
PRK10803	263	tol-pal system protein YbgF; Provisional	97.14
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.08
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.08
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.07
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.02
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.02
KOG0553	304	consensus TPR repeat-containing protein [General f	97.01
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.99
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.96
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.95
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.92
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.91
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.89
PF12688	120	TPR_5: Tetratrico peptide repeat	96.87
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.85
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.84
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.8
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	96.76
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.76
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.72
KOG3941	406	consensus Intermediate in Toll signal transduction	96.69
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.63
PF13371	73	TPR_9: Tetratricopeptide repeat	96.62
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.53
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.53
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.52
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.46
KOG0553	304	consensus TPR repeat-containing protein [General f	96.35
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.33
PF12688	120	TPR_5: Tetratrico peptide repeat	96.32
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.3
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.28
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.23
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.21
KOG3941	406	consensus Intermediate in Toll signal transduction	96.19
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.13
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.07
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.01
PF13371	73	TPR_9: Tetratricopeptide repeat	95.99
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.98
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.96
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.93
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.83
PRK10803	263	tol-pal system protein YbgF; Provisional	95.8
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	95.79
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.62
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.57
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.56
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.51
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.47
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.3
KOG2796	366	consensus Uncharacterized conserved protein [Funct	95.2
PF14669	233	Asp_Glu_race_2: Putative aspartate racemase	95.09
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.06
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	94.74
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	94.73
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.69
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.69
PF13428	44	TPR_14: Tetratricopeptide repeat	94.67
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.61
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	94.44
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	94.33
KOG1585	308	consensus Protein required for fusion of vesicles	94.32
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	94.24
COG4105	254	ComL DNA uptake lipoprotein [General function pred	94.2
PRK15331	165	chaperone protein SicA; Provisional	94.18
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.18
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	94.18
KOG2796	366	consensus Uncharacterized conserved protein [Funct	94.17
COG4700	251	Uncharacterized protein conserved in bacteria cont	94.07
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	93.95
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.9
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.83
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	93.76
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.71
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	93.61
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.55
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	93.49
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.46
PRK15331	165	chaperone protein SicA; Provisional	93.36
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.14
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	93.02
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.01
PF13929	292	mRNA_stabil: mRNA stabilisation	92.95
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	92.82
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	92.79
PF13512	142	TPR_18: Tetratricopeptide repeat	92.42
KOG4555	175	consensus TPR repeat-containing protein [Function	92.39
COG3898	531	Uncharacterized membrane-bound protein [Function u	92.33
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	92.33
KOG2063	877	consensus Vacuolar assembly/sorting proteins VPS39	92.3
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	91.96
PF13428	44	TPR_14: Tetratricopeptide repeat	91.63
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	91.6
COG3629	280	DnrI DNA-binding transcriptional activator of the	91.32
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	91.26
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	90.94
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	90.88
KOG1941	518	consensus Acetylcholine receptor-associated protei	90.81
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.02
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	89.93
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	89.78
KOG4555	175	consensus TPR repeat-containing protein [Function	89.76
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.72
PF13512	142	TPR_18: Tetratricopeptide repeat	89.68
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	89.61
KOG4570	418	consensus Uncharacterized conserved protein [Funct	89.52
COG4105	254	ComL DNA uptake lipoprotein [General function pred	89.51
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	88.36
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	88.27
PRK11906	458	transcriptional regulator; Provisional	88.04
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	87.57
PF13762	145	MNE1: Mitochondrial splicing apparatus component	87.47
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	87.4
COG3118	304	Thioredoxin domain-containing protein [Posttransla	87.16
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	86.64
PF13431	34	TPR_17: Tetratricopeptide repeat	86.27
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	86.23
PRK11906	458	transcriptional regulator; Provisional	86.21
COG3118	304	Thioredoxin domain-containing protein [Posttransla	86.19
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	86.09
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	86.04
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	86.01
PF13431	34	TPR_17: Tetratricopeptide repeat	85.87
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	85.69
KOG1585	308	consensus Protein required for fusion of vesicles	85.48
PF13929	292	mRNA_stabil: mRNA stabilisation	85.38
KOG2610	491	consensus Uncharacterized conserved protein [Funct	85.29
PF13934	226	ELYS: Nuclear pore complex assembly	85.08
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	84.92
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	84.83
KOG4234	271	consensus TPR repeat-containing protein [General f	84.02
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	83.8
PRK13342	413	recombination factor protein RarA; Reviewed	83.27
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	83.23
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	83.16
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	82.88
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	82.75
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	82.56
KOG2610	491	consensus Uncharacterized conserved protein [Funct	82.44
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	82.3
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	82.16
COG4455	273	ImpE Protein of avirulence locus involved in tempe	81.65
COG3947	361	Response regulator containing CheY-like receiver a	81.04
PRK09687	280	putative lyase; Provisional	80.58
COG3898	531	Uncharacterized membrane-bound protein [Function u	80.26

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=5.5e-58  Score=446.82  Aligned_cols=360  Identities=15%  Similarity=0.171  Sum_probs=342.2

Q ss_pred             ccccCCChHHHHHHHHHHHHcccch-hhHHh-----------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHH
Q 040338            3 ACGSLKSLPIARKIHAQLISTCLIS-SIFLQ-----------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         3 ~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~-----------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      .|.+.|+++.|+++|++|.+.++.+ +...+           .+++|.++|+.|+.||..+||.+|.+|++   .|+++.
T Consensus       379 ~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~a~~k---~g~~e~  455 (1060)
T PLN03218        379 RLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCAS---SQDIDG  455 (1060)
T ss_pred             HHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHh---CcCHHH
Confidence            4667899999999999999999654 33332           69999999999999999999999999777   899999


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHH
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISIL  150 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  150 (385)
                      |.++|++|.+.|+.||..+|++||.+|++.|++++|.++|++|.+.|+                  .||..+|+.||.+|
T Consensus       456 A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv------------------~PdvvTynaLI~gy  517 (1060)
T PLN03218        456 ALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGV------------------EANVHTFGALIDGC  517 (1060)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCC------------------CCCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999998                  89999999999999


Q ss_pred             HhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHH--hCCCCchHHHHHHHHHHHhcCCCC-
Q 040338          151 TRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVH--MEPSLDVFVGSGLIDMYLKCGCNG-  227 (385)
Q Consensus       151 ~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~li~~~~~~g~~~-  227 (385)
                      ++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|++|..  .|+.||..+|+++|.+|++.|+.+ 
T Consensus       518 ~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~lde  597 (1060)
T PLN03218        518 ARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDR  597 (1060)
T ss_pred             HHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHH
Confidence            99999999999999999999999999999999999999999999999999987  678999999999999999999876 


Q ss_pred             ------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----CChhhHHHHHHHHHhcCCCCchHHHH-----
Q 040338          228 ------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR----RNMISWMVLISAFSQAGVLEKPRFFF-----  286 (385)
Q Consensus       228 ------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~li~~~~~~g~~~~a~~~~-----  286 (385)
                                  +.|+..+|+.+|.+|++.|++++|.++|++|.+    ||..+|+.+|.+|++.|++++|.+++     
T Consensus       598 A~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k  677 (1060)
T PLN03218        598 AKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK  677 (1060)
T ss_pred             HHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                        789999999999999999999999999999985    79999999999999999999999999     


Q ss_pred             --------HHHHHHHHhcccCChhhHHHHHHHHHhccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---CCcchH
Q 040338          287 --------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---PTCVIW  352 (385)
Q Consensus       287 --------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p~~~~~  352 (385)
                              +|+.+|.+|++.|++++|.++|++|.+.+.   ..+|++||.+|++.|++++|.++|++|...   ||..||
T Consensus       678 ~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty  757 (1060)
T PLN03218        678 QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY  757 (1060)
T ss_pred             cCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence                    999999999999999999999999998776   889999999999999999999999999864   999999


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          353 GALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       353 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ++++.+|++.|++++|.+++++|.+.|+.|.
T Consensus       758 ~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd  788 (1060)
T PLN03218        758 SILLVASERKDDADVGLDLLSQAKEDGIKPN  788 (1060)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            9999999999999999999999999998875

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=6.2e-57  Score=445.26  Aligned_cols=378  Identities=28%  Similarity=0.418  Sum_probs=327.8

Q ss_pred             ccccCCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHH
Q 040338            3 ACGSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMA   71 (385)
Q Consensus         3 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a   71 (385)
                      +|++.+++..++++|.++.+.|+.|+.+++           ++++|.++|++|+.||.++||+||.+|++   .|++++|
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~---~g~~~eA  272 (857)
T PLN03077        196 TCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFE---NGECLEG  272 (857)
T ss_pred             HhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHh---CCCHHHH
Confidence            344444444444445555555555554444           88999999999999999999999999888   9999999


Q ss_pred             HHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcc----ccc---------cchHHHHHHhcCCCCC
Q 040338           72 LHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLF----CWK---------FGIIRLLIMFQKMPER  138 (385)
Q Consensus        72 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~----~~~---------~~~~~a~~~~~~~~~~  138 (385)
                      +++|++|.+.|+.||..||+.+|.+|++.|+++.|.+++..|.+.|..    +++         |++++|.++|++|..|
T Consensus       273 l~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~  352 (857)
T PLN03077        273 LELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK  352 (857)
T ss_pred             HHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCC
Confidence            999999999999999999999999999999999999999999876642    333         9999999999999999


Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHH
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLID  218 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  218 (385)
                      |..+||++|.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|+++.|.++++.|.+.|+.|+..+|++|++
T Consensus       353 d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~  432 (857)
T PLN03077        353 DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIE  432 (857)
T ss_pred             CeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCC---------C----------------------------------CchhhHH--------------------
Q 040338          219 MYLKCGCNG---------I----------------------------------ESSIQIG--------------------  235 (385)
Q Consensus       219 ~~~~~g~~~---------~----------------------------------~~~~~~~--------------------  235 (385)
                      +|++.|+.+         .                                  .||..||                    
T Consensus       433 ~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~  512 (857)
T PLN03077        433 MYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIH  512 (857)
T ss_pred             HHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHH
Confidence            999999766         2                                  3333333                    


Q ss_pred             ---------------HHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH-------------H
Q 040338          236 ---------------KALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF-------------F  287 (385)
Q Consensus       236 ---------------~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~-------------~  287 (385)
                                     ++||++|+++|++++|.++|+.| ++|..+||+||.+|+++|+.++|+++|             |
T Consensus       513 ~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T  591 (857)
T PLN03077        513 AHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVT  591 (857)
T ss_pred             HHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCccc
Confidence                           34445666667777777777777 778889999999999999999999999             9


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHH-hccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMA-KFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~-~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g  363 (385)
                      |+.++.+|++.|++++|.++|+.|. +.+.   ..+|+.++++|+++|++++|.+++++|.-+||..+|++|+.+|..+|
T Consensus       592 ~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~pd~~~~~aLl~ac~~~~  671 (857)
T PLN03077        592 FISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHR  671 (857)
T ss_pred             HHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Confidence            9999999999999999999999998 4555   67999999999999999999999999987899999999999998888


Q ss_pred             ChHHHHHHHHHHHhccccCCC
Q 040338          364 NTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      +.+.+....+++.+..|.+++
T Consensus       672 ~~e~~e~~a~~l~~l~p~~~~  692 (857)
T PLN03077        672 HVELGELAAQHIFELDPNSVG  692 (857)
T ss_pred             ChHHHHHHHHHHHhhCCCCcc
Confidence            888888888888887776553

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

Probab=100.00  E-value=6.2e-57  Score=435.52  Aligned_cols=378  Identities=19%  Similarity=0.268  Sum_probs=354.7

Q ss_pred             CcccccCCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChH
Q 040338            1 MKACGSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIK   69 (385)
Q Consensus         1 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~   69 (385)
                      |++|++.++++.|+++|..|.+.|+.|+.+++           ++++|.++|++|+.||.++||++|.+|++   .|+++
T Consensus       130 l~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~---~g~~~  206 (697)
T PLN03081        130 VEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVD---AGNYR  206 (697)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHH---CcCHH
Confidence            35789999999999999999999999999887           99999999999999999999999999888   89999


Q ss_pred             HHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc----cccc---------cchHHHHHHhcCCC
Q 040338           70 MALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL----FCWK---------FGIIRLLIMFQKMP  136 (385)
Q Consensus        70 ~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~~~~---------~~~~~a~~~~~~~~  136 (385)
                      +|.++|++|.+.|+.|+..+|+.++.+|++.|..+.+.+++..+.+.|.    .+++         |++++|.++|++|+
T Consensus       207 ~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~  286 (697)
T PLN03081        207 EAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP  286 (697)
T ss_pred             HHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCC
Confidence            9999999999999999999999999999999999999999998877654    2333         99999999999999


Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      ++|+.+||+||.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|++++|.++++.|.+.|+.||..+|++|
T Consensus       287 ~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~L  366 (697)
T PLN03081        287 EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTAL  366 (697)
T ss_pred             CCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCC---------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----CChhhHHHHHHHHHhcCCCCchH
Q 040338          217 IDMYLKCGCNG---------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR----RNMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       217 i~~~~~~g~~~---------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~li~~~~~~g~~~~a~  283 (385)
                      +++|+++|+.+         ..||..+|++||.+|++.|+.++|.++|++|.+    ||..||+.++.+|++.|..++|.
T Consensus       367 i~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~  446 (697)
T PLN03081        367 VDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGW  446 (697)
T ss_pred             HHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHH
Confidence            99999999877         679999999999999999999999999999975    89999999999999999999999


Q ss_pred             HHH--------------HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-
Q 040338          284 FFF--------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-  347 (385)
Q Consensus       284 ~~~--------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-  347 (385)
                      ++|              +|+.++++|++.|++++|.+++++|...+...+|++++.+|+..|+++.|.++++++.+. | 
T Consensus       447 ~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~  526 (697)
T PLN03081        447 EIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPE  526 (697)
T ss_pred             HHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCC
Confidence            998              899999999999999999999998865555888999999999999999999999998763 5 


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          348 TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       348 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      +..+|..|++.|++.|++++|.+++++|.+.|+.
T Consensus       527 ~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~  560 (697)
T PLN03081        527 KLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLS  560 (697)
T ss_pred             CCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCc
Confidence            4679999999999999999999999999999875

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.2e-56  Score=443.30  Aligned_cols=377  Identities=21%  Similarity=0.291  Sum_probs=301.7

Q ss_pred             cccccCCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHH
Q 040338            2 KACGSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         2 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      ++|.+.+.++.|+++|+++.+.+..++.+++           ++++|+++|++|++||.++||++|.+|++   .|++++
T Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~n~li~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~~~~~---~g~~~~  170 (857)
T PLN03077         94 RLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAK---AGYFDE  170 (857)
T ss_pred             HHHhhCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHHHHHh---CCCHHH
Confidence            3466667777777777777777766665544           78999999999999999999999999888   899999


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc----cccc---------cchHHHHHHhcCCCC
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL----FCWK---------FGIIRLLIMFQKMPE  137 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~~~~---------~~~~~a~~~~~~~~~  137 (385)
                      |.++|++|.+.|+.||..||+++|++|++.++++.+.+++..|.+.|.    .+++         |+++.|.++|++|+.
T Consensus       171 A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~  250 (857)
T PLN03077        171 ALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR  250 (857)
T ss_pred             HHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCC
Confidence            999999999999999999999999999999999999999999976654    2333         999999999999999


Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      ||..+||++|.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|+.+.|.+++..|.+.|+.||..+|++|+
T Consensus       251 ~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li  330 (857)
T PLN03077        251 RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLI  330 (857)
T ss_pred             CCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCC----------------------------------------------------------------------
Q 040338          218 DMYLKCGCNG----------------------------------------------------------------------  227 (385)
Q Consensus       218 ~~~~~~g~~~----------------------------------------------------------------------  227 (385)
                      ++|++.|+.+                                                                      
T Consensus       331 ~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~  410 (857)
T PLN03077        331 QMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVK  410 (857)
T ss_pred             HHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHH
Confidence            9999999766                                                                      


Q ss_pred             ---------CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH------------
Q 040338          228 ---------IESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF------------  286 (385)
Q Consensus       228 ---------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~------------  286 (385)
                               ..|+..+|++||++|+++|++++|.++|++|.++|+.+|+++|.+|++.|+.++|+.+|            
T Consensus       411 l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~  490 (857)
T PLN03077        411 LHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSV  490 (857)
T ss_pred             HHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHh
Confidence                     33445555555555555556666666666665556666666666666666666666555            


Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcC
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHY  363 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g  363 (385)
                      +|+.++.+|++.|+++.+.+++..+.+.|.   ..++++||++|+++|++++|.++|+++  .||..+|+++|.+|+++|
T Consensus       491 t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~--~~d~~s~n~lI~~~~~~G  568 (857)
T PLN03077        491 TLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH--EKDVVSWNILLTGYVAHG  568 (857)
T ss_pred             HHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhc--CCChhhHHHHHHHHHHcC
Confidence            555566555555555555555555555555   555667777777777777777777777  567777777777777777


Q ss_pred             ChHHHHHHHHHHHhccccCC
Q 040338          364 NTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +.++|.++|++|.+.|+.|.
T Consensus       569 ~~~~A~~lf~~M~~~g~~Pd  588 (857)
T PLN03077        569 KGSMAVELFNRMVESGVNPD  588 (857)
T ss_pred             CHHHHHHHHHHHHHcCCCCC
Confidence            77777777777777777664

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.4e-54  Score=421.33  Aligned_cols=379  Identities=15%  Similarity=0.138  Sum_probs=338.7

Q ss_pred             CcccccCCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhC----CCChhhHHHHHHHHHhhhcc
Q 040338            1 MKACGSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIG----PRYLFTYNTMINGGVRCLCV   65 (385)
Q Consensus         1 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~----~~~~~~~~~li~~~~~~~~~   65 (385)
                      |++|++.|+++.|+.+|++|.+.|+.|+.+++           ++++|.++|++|.    .||..+|++||.+|++   .
T Consensus       444 L~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k---~  520 (1060)
T PLN03218        444 MSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR---A  520 (1060)
T ss_pred             HHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH---C
Confidence            46789999999999999999999999998888           9999999999998    6899999999999888   8


Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccC------CCccccc---------cchHHHHH
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLN------PSLFCWK---------FGIIRLLI  130 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~------~~~~~~~---------~~~~~a~~  130 (385)
                      |++++|.++|++|.+.|+.||..+|+.||.+|++.|++++|.++|++|..      ++..+++         |++++|.+
T Consensus       521 G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~e  600 (1060)
T PLN03218        521 GQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKE  600 (1060)
T ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999964      3444444         99999999


Q ss_pred             HhcCCC----CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          131 MFQKMP----ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       131 ~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      +|++|.    +|+..+||.+|.+|++.|++++|.++|++|.+.|+.||..||+.++.+|++.|++++|.+++++|.+.|+
T Consensus       601 lf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~  680 (1060)
T PLN03218        601 VYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGI  680 (1060)
T ss_pred             HHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence            999885    5778899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchHHHHHHHHHHHhcCCCC-------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----CChhhHHHH
Q 040338          207 SLDVFVGSGLIDMYLKCGCNG-------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR----RNMISWMVL  269 (385)
Q Consensus       207 ~~~~~~~~~li~~~~~~g~~~-------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~l  269 (385)
                      .|+..+|++||.+|++.|+.+             ..||..+|++||.+|++.|++++|.++|++|.+    ||..+|+.+
T Consensus       681 ~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sL  760 (1060)
T PLN03218        681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSIL  760 (1060)
T ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            999999999999999999766             689999999999999999999999999999974    799999999


Q ss_pred             HHHHHhcCCCCchHHHH-------------HHHHHHHHhcc-----------------------cCChhhHHHHHHHHHh
Q 040338          270 ISAFSQAGVLEKPRFFF-------------FFVSLLSGCSH-----------------------SGPVTKGKHYFTAMAK  313 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~-------------~~~~l~~~~~~-----------------------~~~~~~a~~~~~~~~~  313 (385)
                      +.+|++.|++++|.+++             +|+.++..|.+                       .+..+.|..+|++|.+
T Consensus       761 L~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~  840 (1060)
T PLN03218        761 LVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETIS  840 (1060)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHH
Confidence            99999999999999998             78888876542                       1223678999999999


Q ss_pred             ccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCCC
Q 040338          314 FTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       314 ~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      .|.   ..+|+.++.++++.+..+.+..++++|...   |+..+|+++|.++.+.  .++|..++++|.+.|+.|..
T Consensus       841 ~Gi~Pd~~T~~~vL~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~~--~~~A~~l~~em~~~Gi~p~~  915 (1060)
T PLN03218        841 AGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEY--DPRAFSLLEEAASLGVVPSV  915 (1060)
T ss_pred             CCCCCCHHHHHHHHHHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhccC--hHHHHHHHHHHHHcCCCCCc
Confidence            998   778999998888999999999999988764   7788999999998432  36899999999999998863

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

Probab=100.00  E-value=5.3e-53  Score=408.18  Aligned_cols=371  Identities=22%  Similarity=0.257  Sum_probs=326.1

Q ss_pred             cccccCCChHHHHHHHHHHHHcc-cchhhHHh-----------hhhhHHHHHhhhC----CCChhhHHHHHHHHHhhhcc
Q 040338            2 KACGSLKSLPIARKIHAQLISTC-LISSIFLQ-----------LIDDDYRVFCDIG----PRYLFTYNTMINGGVRCLCV   65 (385)
Q Consensus         2 ~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~-----------~~~~A~~~~~~~~----~~~~~~~~~li~~~~~~~~~   65 (385)
                      .++.+.|++++|..+|++|...+ +.|+.+++           +++.|..++..|.    .||+.+||.+|..|++   .
T Consensus        95 ~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k---~  171 (697)
T PLN03081         95 EKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVK---C  171 (697)
T ss_pred             HHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhc---C
Confidence            35667788888888888888764 56666665           6777777887775    5788888888888777   6


Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcc----ccc---------cchHHHHHHh
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLF----CWK---------FGIIRLLIMF  132 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~----~~~---------~~~~~a~~~~  132 (385)
                      |+++.|.++|++|.    .||..+||++|.+|++.|++++|.++|++|.+.+..    ++.         |..+.+.+++
T Consensus       172 g~~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~  247 (697)
T PLN03081        172 GMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLH  247 (697)
T ss_pred             CCHHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHH
Confidence            88888888888885    468888888888888888888888888888665442    222         5666666665


Q ss_pred             cCC----CCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCC
Q 040338          133 QKM----PERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL  208 (385)
Q Consensus       133 ~~~----~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  208 (385)
                      ..+    ..||..+||+||.+|++.|++++|.++|++|.    .+|..+|+.+|.+|++.|+.++|.++|++|.+.|+.|
T Consensus       248 ~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~p  323 (697)
T PLN03081        248 CCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSI  323 (697)
T ss_pred             HHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCC
Confidence            444    35889999999999999999999999999994    5799999999999999999999999999999999999


Q ss_pred             chHHHHHHHHHHHhcCCCC-------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHh
Q 040338          209 DVFVGSGLIDMYLKCGCNG-------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQ  275 (385)
Q Consensus       209 ~~~~~~~li~~~~~~g~~~-------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~  275 (385)
                      |..+|++++.+|++.|+.+             ..||..+|++||++|+++|++++|.++|++|.+||+.+||+||.+|++
T Consensus       324 d~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~  403 (697)
T PLN03081        324 DQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGN  403 (697)
T ss_pred             CHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHH
Confidence            9999999999999999877             799999999999999999999999999999999999999999999999


Q ss_pred             cCCCCchHHHH-------------HHHHHHHHhcccCChhhHHHHHHHHHhc-cc---hhhHHHHHHHHHccCCHHHHHH
Q 040338          276 AGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKHYFTAMAKF-TY---TCYFVCMVDLLGLSGLLGEAKK  338 (385)
Q Consensus       276 ~g~~~~a~~~~-------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~---~~~~~~li~~~~~~g~~~~A~~  338 (385)
                      +|+.++|+++|             ||+.++.+|++.|++++|.++|+.|.+. +.   ..+|+.++++|+++|++++|.+
T Consensus       404 ~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~  483 (697)
T PLN03081        404 HGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYA  483 (697)
T ss_pred             cCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHH
Confidence            99999999999             9999999999999999999999999874 44   6799999999999999999999


Q ss_pred             HHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          339 LIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       339 ~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ++++|..+|+..+|++|+.+|..+|+.+.|..+++++.+.+|.+.
T Consensus       484 ~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~  528 (697)
T PLN03081        484 MIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKL  528 (697)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCC
Confidence            999999889999999999999999999999999999998888654

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

Probab=99.93  E-value=2e-22  Score=202.60  Aligned_cols=371  Identities=11%  Similarity=-0.014  Sum_probs=223.7

Q ss_pred             cccCCChHHHHHHHHHHHHcccch-hhHHh---------hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHH
Q 040338            4 CGSLKSLPIARKIHAQLISTCLIS-SIFLQ---------LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~---------~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      +.+.|+++.|..+++.+....... ..+..         ++++|...|+++.   +.+...+..+...+..   .|++++
T Consensus       441 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~---~g~~~~  517 (899)
T TIGR02917       441 YLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQ---EGNPDD  517 (899)
T ss_pred             HHhcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHH---CCCHHH
Confidence            456677777877777777654321 11111         7777777777654   2234445555555544   677777


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcccc------------ccchHHHHHHhcCCC--
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW------------KFGIIRLLIMFQKMP--  136 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~------------~~~~~~a~~~~~~~~--  136 (385)
                      |.+.++.+.+.+ +.+..++..+...+.+.|+.++|...++++.+.+....            .|+.++|..++.++.  
T Consensus       518 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  596 (899)
T TIGR02917       518 AIQRFEKVLTID-PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADA  596 (899)
T ss_pred             HHHHHHHHHHhC-cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            777777777654 33566677777777777777777777777644332111            166677776666653  


Q ss_pred             -CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          137 -ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       137 -~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                       +.+...|..+..++.+.|++++|...|+++.+.. +.+...+..+..++.+.|++++|..+++.+.+.. +.+..++..
T Consensus       597 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~  674 (899)
T TIGR02917       597 APDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIG  674 (899)
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHH
Confidence             3455667777777777777777777777776542 2245556666667777777777777777776653 234556666


Q ss_pred             HHHHHHhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCc
Q 040338          216 LIDMYLKCGCNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEK  281 (385)
Q Consensus       216 li~~~~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~  281 (385)
                      +...+...|+.+            .+.+...+..+...+...|++++|...|+.+.+  |+..++..++.++.+.|++++
T Consensus       675 l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  754 (899)
T TIGR02917       675 LAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAE  754 (899)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHH
Confidence            666666666554            334455566666666666666666666666543  444555556666666666666


Q ss_pred             hHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-
Q 040338          282 PRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-  346 (385)
Q Consensus       282 a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  346 (385)
                      |.+.+            .+..+...|...|+.++|.+.|+++.+..+  +..++.+...+...|+ ++|+.++++.... 
T Consensus       755 A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~  833 (899)
T TIGR02917       755 AVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKALKLA  833 (899)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhC
Confidence            66555            555555666666666666666666665554  4455555555555555 5555555554432 


Q ss_pred             C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          347 P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       347 p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      | +..++..+...+...|++++|...++++++.+|.
T Consensus       834 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~  869 (899)
T TIGR02917       834 PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE  869 (899)
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            2 2334445555555555555555555555555543

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=99.92  E-value=3.1e-22  Score=201.15  Aligned_cols=365  Identities=13%  Similarity=0.003  Sum_probs=193.9

Q ss_pred             ccCCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHH
Q 040338            5 GSLKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMA   71 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a   71 (385)
                      ...|+++.|...++++.+..........          ++++|...|+++.   +.+..++..+...+..   .|+.++|
T Consensus       476 ~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~A  552 (899)
T TIGR02917       476 LGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLR---TGNEEEA  552 (899)
T ss_pred             HhCCCHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHH---cCCHHHH
Confidence            3445566666666655543322111111          5555666655543   2234445555555444   5566666


Q ss_pred             HHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcc---ccc---------cchHHHHHHhcCCC---
Q 040338           72 LHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLF---CWK---------FGIIRLLIMFQKMP---  136 (385)
Q Consensus        72 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~---~~~---------~~~~~a~~~~~~~~---  136 (385)
                      ..+++++.+.+ +.+...+..++..|.+.|++++|..+++++.+....   .|.         |++++|...|.++.   
T Consensus       553 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  631 (899)
T TIGR02917       553 VAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ  631 (899)
T ss_pred             HHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            66666655543 234445555556666666666666666555432221   111         55555555555442   


Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      +.+...+..+...+.+.|++++|..+|+++.+. .+.+..++..+...+...|++++|.++++.+.+.+ +.+...+..+
T Consensus       632 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~  709 (899)
T TIGR02917       632 PDSALALLLLADAYAVMKNYAKAITSLKRALEL-KPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELE  709 (899)
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHH
Confidence            223445555555566666666666666655543 12234555555555666666666666666655543 2344455555


Q ss_pred             HHHHHhcCCCC-----------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCch
Q 040338          217 IDMYLKCGCNG-----------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKP  282 (385)
Q Consensus       217 i~~~~~~g~~~-----------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a  282 (385)
                      ...+.+.|+++           ..|+..++..+...+.+.|++++|.+.++.+.+   .+...+..+...|...|+.++|
T Consensus       710 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A  789 (899)
T TIGR02917       710 GDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKA  789 (899)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHH
Confidence            55555555444           334445555555666666666666666555543   2444555555556666666666


Q ss_pred             HHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C
Q 040338          283 RFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P  347 (385)
Q Consensus       283 ~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p  347 (385)
                      .+.+            ++..+...+...|+ .+|...++++....+  +..+..+...+...|++++|.+.|+++.+. |
T Consensus       790 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~  868 (899)
T TIGR02917       790 IKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAP  868 (899)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            5555            45555555555555 556666665555444  444455555555666666666666655543 2


Q ss_pred             -CcchHHHHHHHHHhcCChHHHHHHHHHHH
Q 040338          348 -TCVIWGALLGACCSHYNTKLAELVMRNLL  376 (385)
Q Consensus       348 -~~~~~~~li~~~~~~g~~~~a~~~~~~~~  376 (385)
                       +..++..+..++.+.|+.++|.+++++|+
T Consensus       869 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       869 EAAAIRYHLALALLATGRKAEARKELDKLL  898 (899)
T ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence             44555556666666666666666665554

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=99.88  E-value=9.9e-20  Score=165.60  Aligned_cols=281  Identities=12%  Similarity=0.035  Sum_probs=218.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC---Ccc
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER---DLV  141 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~---~~~  141 (385)
                      .|++++|...|+++.+.+ +.+..++..+...+...|++++|..+++.+.....                  .+   ...
T Consensus        48 ~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~------------------~~~~~~~~  108 (389)
T PRK11788         48 NEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPD------------------LTREQRLL  108 (389)
T ss_pred             cCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCC------------------CCHHHHHH
Confidence            688888999998888864 33566788888888888889888888888765331                  11   124


Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYL  221 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  221 (385)
                      ++..+...|.+.|++++|..+|+++.+. -+++..++..++..+.+.|++++|.+.++.+.+.+..+....         
T Consensus       109 ~~~~La~~~~~~g~~~~A~~~~~~~l~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~---------  178 (389)
T PRK11788        109 ALQELGQDYLKAGLLDRAEELFLQLVDE-GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVE---------  178 (389)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHH---------
Confidence            6777888888888888888888888764 234567788888888888888888888888887654332210         


Q ss_pred             hcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------
Q 040338          222 KCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------  286 (385)
Q Consensus       222 ~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------  286 (385)
                               ....+..+...+.+.|++++|...|+++.+  | +...+..+...+.+.|++++|++.+            
T Consensus       179 ---------~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~  249 (389)
T PRK11788        179 ---------IAHFYCELAQQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLS  249 (389)
T ss_pred             ---------HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHH
Confidence                     111235566677778888888888888765  3 3456777788888888888888887            


Q ss_pred             -HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHh--
Q 040338          287 -FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACCS--  361 (385)
Q Consensus       287 -~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~--  361 (385)
                       ++..+..+|...|++++|...++++.+..+ ...+..++..+.+.|++++|.++++++.+. |+..++..++..+..  
T Consensus       250 ~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~  329 (389)
T PRK11788        250 EVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEA  329 (389)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhcc
Confidence             467788899999999999999999988777 555688999999999999999999988765 999999998888775  


Q ss_pred             -cCChHHHHHHHHHHHhccccCC
Q 040338          362 -HYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       362 -~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                       .|+.+++..+++++.+.++.+.
T Consensus       330 ~~g~~~~a~~~~~~~~~~~~~~~  352 (389)
T PRK11788        330 EEGRAKESLLLLRDLVGEQLKRK  352 (389)
T ss_pred             CCccchhHHHHHHHHHHHHHhCC
Confidence             5589999999999998665543

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.82  E-value=6.4e-18  Score=153.72  Aligned_cols=268  Identities=13%  Similarity=0.070  Sum_probs=216.8

Q ss_pred             hhhhHHHHHhhhC--CC-ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC---chHHHhHHHHHHhcCChhHH
Q 040338           33 LIDDDYRVFCDIG--PR-YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD---ESIAKSSIDMHVKCGAVDYA  106 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~li~~~~~~g~~~~a  106 (385)
                      ++++|...|+++.  .| +..++..+...+..   .|++++|..+++.+.+.+..++   ...+..+...|.+.|++++|
T Consensus        50 ~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~---~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A  126 (389)
T PRK11788         50 QPDKAIDLFIEMLKVDPETVELHLALGNLFRR---RGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRA  126 (389)
T ss_pred             ChHHHHHHHHHHHhcCcccHHHHHHHHHHHHH---cCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            8889999999887  33 34567777777666   8999999999999987542221   25678889999999999999


Q ss_pred             HHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH----hhHHHHH
Q 040338          107 ESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS----MLYATAF  182 (385)
Q Consensus       107 ~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~ll  182 (385)
                      ..+|+++.+.+                   +++..+++.++..+.+.|++++|.+.++.+.+.+..++.    ..+..+.
T Consensus       127 ~~~~~~~l~~~-------------------~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la  187 (389)
T PRK11788        127 EELFLQLVDEG-------------------DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELA  187 (389)
T ss_pred             HHHHHHHHcCC-------------------cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHH
Confidence            99999987654                   467789999999999999999999999999886543322    2355677


Q ss_pred             HHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--
Q 040338          183 SARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--  260 (385)
Q Consensus       183 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--  260 (385)
                      ..+.+.|++++|.+.++++.+...  +                     +...+..+...+.+.|++++|.++|+++.+  
T Consensus       188 ~~~~~~~~~~~A~~~~~~al~~~p--~---------------------~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  244 (389)
T PRK11788        188 QQALARGDLDAARALLKKALAADP--Q---------------------CVRASILLGDLALAQGDYAAAIEALERVEEQD  244 (389)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhHCc--C---------------------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            788899999999999999987642  2                     123445677788888899999999999885  


Q ss_pred             CC--hhhHHHHHHHHHhcCCCCchHHHH-----------HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHH
Q 040338          261 RN--MISWMVLISAFSQAGVLEKPRFFF-----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDL  326 (385)
Q Consensus       261 ~~--~~~~~~li~~~~~~g~~~~a~~~~-----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~  326 (385)
                      |+  ..+++.++.+|...|++++|...+           .+..+...+.+.|++++|..+++++.+..+ ...+..++..
T Consensus       245 p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~  324 (389)
T PRK11788        245 PEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDY  324 (389)
T ss_pred             hhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence            33  346788899999999999999988           568889999999999999999999888877 6677777777


Q ss_pred             HHc---cCCHHHHHHHHHhCCC
Q 040338          327 LGL---SGLLGEAKKLIDEMPS  345 (385)
Q Consensus       327 ~~~---~g~~~~A~~~~~~m~~  345 (385)
                      +..   .|+.+++..++++|.+
T Consensus       325 ~~~~~~~g~~~~a~~~~~~~~~  346 (389)
T PRK11788        325 HLAEAEEGRAKESLLLLRDLVG  346 (389)
T ss_pred             hhhccCCccchhHHHHHHHHHH
Confidence            664   5689999999998875

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.81  E-value=1.2e-16  Score=153.00  Aligned_cols=303  Identities=10%  Similarity=-0.072  Sum_probs=223.1

Q ss_pred             hhhhHHHHHhhhC--CCC-hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG--PRY-LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|..+++...  .|+ ......+..+...   .|+++.|...++.+.+.. +.+...+..+...+.+.|+.++|...
T Consensus        57 ~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~---~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~  132 (656)
T PRK15174         57 ETDVGLTLLSDRVLTAKNGRDLLRRWVISPLA---SSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADL  132 (656)
T ss_pred             CcchhHHHhHHHHHhCCCchhHHHHHhhhHhh---cCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHH
Confidence            7777777776654  333 2333334444333   799999999999998864 33567788888888889999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY  189 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~  189 (385)
                      |++..+..                   +.+...+..+...+...|++++|...++.+......+ ...+..+ ..+...|
T Consensus       133 l~~Al~l~-------------------P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~~-~~l~~~g  191 (656)
T PRK15174        133 AEQAWLAF-------------------SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIATC-LSFLNKS  191 (656)
T ss_pred             HHHHHHhC-------------------CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHHH-HHHHHcC
Confidence            98876654                   3566778888888999999999999998886653222 2233233 3467788


Q ss_pred             CccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhH
Q 040338          190 DLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISW  266 (385)
Q Consensus       190 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~  266 (385)
                      ++++|...++.+++....++...                      +..+...+.+.|++++|+..++...+  | +...+
T Consensus       192 ~~~eA~~~~~~~l~~~~~~~~~~----------------------~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~  249 (656)
T PRK15174        192 RLPEDHDLARALLPFFALERQES----------------------AGLAVDTLCAVGKYQEAIQTGESALARGLDGAALR  249 (656)
T ss_pred             CHHHHHHHHHHHHhcCCCcchhH----------------------HHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHH
Confidence            99999998888877643222222                      23345566677888899888888765  2 55677


Q ss_pred             HHHHHHHHhcCCCCc----hHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHH
Q 040338          267 MVLISAFSQAGVLEK----PRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLG  328 (385)
Q Consensus       267 ~~li~~~~~~g~~~~----a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~  328 (385)
                      ..+...+...|++++    |+..+            .+..+...+...|++++|...+++.....+  ......+...|.
T Consensus       250 ~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~  329 (656)
T PRK15174        250 RSLGLAYYQSGRSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALR  329 (656)
T ss_pred             HHHHHHHHHcCCchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            778888888888886    56666            778888888899999999999999888777  666777888899


Q ss_pred             ccCCHHHHHHHHHhCCCC-CCcch-HHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          329 LSGLLGEAKKLIDEMPSK-PTCVI-WGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       329 ~~g~~~~A~~~~~~m~~~-p~~~~-~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +.|++++|...|+++... |+... +..+..++...|+.++|...+++..+..|..
T Consensus       330 ~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~~  385 (656)
T PRK15174        330 QVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQARASH  385 (656)
T ss_pred             HCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChhh
Confidence            999999999999888764 66544 3345677888999999999999988877653

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

Probab=99.79  E-value=9e-17  Score=142.48  Aligned_cols=306  Identities=13%  Similarity=0.084  Sum_probs=210.1

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc--cccc----
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL--FCWK----  122 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~--~~~~----  122 (385)
                      ..+|..+-+.+-.   +|++++|+.+++.+++.. +-.+..|..+..++...|+.+.|.+.|.+..+.++  ++..    
T Consensus       116 ae~ysn~aN~~ke---rg~~~~al~~y~~aiel~-p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lg  191 (966)
T KOG4626|consen  116 AEAYSNLANILKE---RGQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLG  191 (966)
T ss_pred             HHHHHHHHHHHHH---hchHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchh
Confidence            4466666666555   777888888887777753 22566777777777777777777777766655443  1111    


Q ss_pred             ----------------------------------------cchHHHHHHhcCCCCCC---cchHHHHHHHHHhCCCchHH
Q 040338          123 ----------------------------------------FGIIRLLIMFQKMPERD---LVSWNTMISILTRHGFGFET  159 (385)
Q Consensus       123 ----------------------------------------~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~a  159 (385)
                                                              |++..|+..|.+-.+.|   ...|-.|-..|...+.+++|
T Consensus       192 nLlka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~ke~~~~d~A  271 (966)
T KOG4626|consen  192 NLLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVYKEARIFDRA  271 (966)
T ss_pred             HHHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHHHHHhcchHH
Confidence                                                    55555555555543322   23455555555555556666


Q ss_pred             HHHHHHHHHCCCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHH
Q 040338          160 LCTFIELWNHGFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKAL  238 (385)
Q Consensus       160 ~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~l  238 (385)
                      +..|.+...  ..|+ ...|..+...|...|+++.|+..+++.+...+                       .-...|+.|
T Consensus       272 vs~Y~rAl~--lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P-----------------------~F~~Ay~Nl  326 (966)
T KOG4626|consen  272 VSCYLRALN--LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQP-----------------------NFPDAYNNL  326 (966)
T ss_pred             HHHHHHHHh--cCCcchhhccceEEEEeccccHHHHHHHHHHHHhcCC-----------------------CchHHHhHH
Confidence            655555543  2443 34455555555555666666666655554322                       123567888


Q ss_pred             HHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhh
Q 040338          239 VTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTK  303 (385)
Q Consensus       239 i~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~  303 (385)
                      ..++-..|++.+|.+.|++...  | ...+.+.|...|...|.+++|..+|            ..+.+...|...|++++
T Consensus       327 anALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~  406 (966)
T KOG4626|consen  327 ANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDD  406 (966)
T ss_pred             HHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHH
Confidence            8888888888888888887765  3 4567788888888888888888887            77888888888888888


Q ss_pred             HHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCC-cchHHHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          304 GKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPT-CVIWGALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       304 a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      |+..+++..+..+  ...|+-+...|-..|+.+.|.+.+.+... +|. ...++.|...|-..|+..+|++-+++.++..
T Consensus       407 Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklk  486 (966)
T KOG4626|consen  407 AIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLK  486 (966)
T ss_pred             HHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccC
Confidence            8888888888777  78888888888888888888888877765 354 3467888888888888888888888888877


Q ss_pred             ccCC
Q 040338          380 VKVF  383 (385)
Q Consensus       380 ~~~~  383 (385)
                      |.-+
T Consensus       487 PDfp  490 (966)
T KOG4626|consen  487 PDFP  490 (966)
T ss_pred             CCCc
Confidence            7643

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.78  E-value=1.4e-15  Score=155.16  Aligned_cols=369  Identities=10%  Similarity=-0.048  Sum_probs=265.0

Q ss_pred             cccCCChHHHHHHHHHHHHcccc-hhhHHh---------hhhhHHHHHhhhC--CCCh---hhHHHHHH---------HH
Q 040338            4 CGSLKSLPIARKIHAQLISTCLI-SSIFLQ---------LIDDDYRVFCDIG--PRYL---FTYNTMIN---------GG   59 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~---------~~~~A~~~~~~~~--~~~~---~~~~~li~---------~~   59 (385)
                      +...|++++|...++++++.... +.....         ++++|...|++..  .|+.   ..|..++.         ..
T Consensus       279 ~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g  358 (1157)
T PRK11447        279 AVDSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQG  358 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHH
Confidence            34579999999999999986543 222222         8999999998765  2332   22333221         11


Q ss_pred             HhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcccc-----------ccchHHH
Q 040338           60 VRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW-----------KFGIIRL  128 (385)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~-----------~~~~~~a  128 (385)
                      ..+...|++++|...+++..+.. +.+...+..+..++...|++++|++.|++..+.+....           .+..++|
T Consensus       359 ~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~~~~~~~A  437 (1157)
T PRK11447        359 DAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYRQQSPEKA  437 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHH
Confidence            11234899999999999999874 34567788889999999999999999999876443111           1556777


Q ss_pred             HHHhcCCCCCC------------cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchh
Q 040338          129 LIMFQKMPERD------------LVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGP  195 (385)
Q Consensus       129 ~~~~~~~~~~~------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~  195 (385)
                      +..+..++...            ...+..+...+...|++++|++.|++..+.  .| +...+..+...+.+.|++++|.
T Consensus       438 ~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~--~P~~~~~~~~LA~~~~~~G~~~~A~  515 (1157)
T PRK11447        438 LAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLAL--DPGSVWLTYRLAQDLRQAGQRSQAD  515 (1157)
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            77777665321            223455667788899999999999999875  45 4566778888999999999999


Q ss_pred             hHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC-------------CCchh---------hHHHHHHHHHHcCCChhHHHH
Q 040338          196 HLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG-------------IESSI---------QIGKALVTMYAEGGSTQKADL  253 (385)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~-------------~~~~~---------~~~~~li~~~~~~g~~~~A~~  253 (385)
                      ..++.+.+..+. +...+..+...+...++.+             ..++.         ..+..+...+...|+.++|+.
T Consensus       516 ~~l~~al~~~P~-~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~  594 (1157)
T PRK11447        516 ALMRRLAQQKPN-DPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEA  594 (1157)
T ss_pred             HHHHHHHHcCCC-CHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHH
Confidence            999999876543 3333333333333334322             11111         112345667888899999999


Q ss_pred             HHHhcccCChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhh
Q 040338          254 AFELMSRRNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCY  319 (385)
Q Consensus       254 ~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~  319 (385)
                      +++.- ..+...+..+...+.+.|++++|++.+            .+..+...+...|+.++|.+.++...+..+  ...
T Consensus       595 ~l~~~-p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~  673 (1157)
T PRK11447        595 LLRQQ-PPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNT  673 (1157)
T ss_pred             HHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHH
Confidence            98832 235566777888899999999999888            788888889999999999999998887665  566


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhCCCC-CC-------cchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-------CVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-------~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      ...+..++...|++++|.++++.+... |+       ...+..+...+...|++++|+..|++...
T Consensus       674 ~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        674 QRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            677788888999999999999988763 21       23566677888999999999999998865

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.76  E-value=3.6e-15  Score=126.99  Aligned_cols=350  Identities=13%  Similarity=0.024  Sum_probs=242.7

Q ss_pred             ccCCChHHHHHHHHHHHHcccchhhHHh--------------------------------------hhhhHHHHHhhhCC
Q 040338            5 GSLKSLPIARKIHAQLISTCLISSIFLQ--------------------------------------LIDDDYRVFCDIGP   46 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~--------------------------------------~~~~A~~~~~~~~~   46 (385)
                      ..+|.+..+.-+.++|.+.|..-+.-+.                                      +-+-|.-+|+..| 
T Consensus       126 IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~~P-  204 (625)
T KOG4422|consen  126 ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFETLP-  204 (625)
T ss_pred             HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhhcC-
Confidence            3467778888888888888754443322                                      3344454555444 


Q ss_pred             CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           47 RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        47 ~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                      .+..||.+||.|+|+   --..++|.+++++-.+...+.+..+||.+|.+-.-.-+    .+++.+|.+..+        
T Consensus       205 KT~et~s~mI~Gl~K---~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm--------  269 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCK---FSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKM--------  269 (625)
T ss_pred             CCchhHHHHHHHHHH---HHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhc--------
Confidence            456789999999999   58899999999999988889999999999976544322    678888887777        


Q ss_pred             HHHHHhcCCCCCCcchHHHHHHHHHhCCCchH----HHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccc-hhhHHHHH
Q 040338          127 RLLIMFQKMPERDLVSWNTMISILTRHGFGFE----TLCTFIELWNHGFGLSSMLYATAFSARASVYDLEW-GPHLHSRV  201 (385)
Q Consensus       127 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~----a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~-a~~~~~~~  201 (385)
                                .||..|+|+++++..+.|+++.    |++++.+|++.|+.|...+|..+|..+.+-++..+ +..++.++
T Consensus       270 ----------~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI  339 (625)
T KOG4422|consen  270 ----------TPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDI  339 (625)
T ss_pred             ----------CCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHH
Confidence                      8999999999999999998875    56889999999999999999999999998887644 55555555


Q ss_pred             HHh----CCC----CchHHHHHHHHHHHhcCCCC-----------------CCch---hhHHHHHHHHHHcCCChhHHHH
Q 040338          202 VHM----EPS----LDVFVGSGLIDMYLKCGCNG-----------------IESS---IQIGKALVTMYAEGGSTQKADL  253 (385)
Q Consensus       202 ~~~----~~~----~~~~~~~~li~~~~~~g~~~-----------------~~~~---~~~~~~li~~~~~~g~~~~A~~  253 (385)
                      ...    .++    .|...|.+.|+.|.+..+..                 +.|+   ..-|..+....+.....+.-..
T Consensus       340 ~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~  419 (625)
T KOG4422|consen  340 QNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLK  419 (625)
T ss_pred             HHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            442    233    25666777777776665444                 3333   2345566677777777888888


Q ss_pred             HHHhccc----CChhhHHHHHHHHHhcCCCCchHHHH--------HHHH-----HHHHhcccC-Ch---h----------
Q 040338          254 AFELMSR----RNMISWMVLISAFSQAGVLEKPRFFF--------FFVS-----LLSGCSHSG-PV---T----------  302 (385)
Q Consensus       254 ~~~~m~~----~~~~~~~~li~~~~~~g~~~~a~~~~--------~~~~-----l~~~~~~~~-~~---~----------  302 (385)
                      .|+.|.-    |+..+...++.+.--.|+++-.-++|        +++.     ++...++.. ..   +          
T Consensus       420 ~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak  499 (625)
T KOG4422|consen  420 WYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAK  499 (625)
T ss_pred             HHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHH
Confidence            8888764    56677777777777777777777777        2221     111222211 11   0          


Q ss_pred             hHHHH-------HHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CCcchHH---HHHHHHHhcCChHH
Q 040338          303 KGKHY-------FTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PTCVIWG---ALLGACCSHYNTKL  367 (385)
Q Consensus       303 ~a~~~-------~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~~~~~~---~li~~~~~~g~~~~  367 (385)
                      -|..+       -.++.+... ....+...-.+.+.|+.++|.++|.-+..+    |-....+   -++.+-...++...
T Consensus       500 ~aad~~e~~e~~~~R~r~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsq  579 (625)
T KOG4422|consen  500 CAADIKEAYESQPIRQRAQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQ  579 (625)
T ss_pred             HHHHHHHHHHhhHHHHHhccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHH
Confidence            01111       112222222 566677777889999999999999887543    3333444   56666677788889


Q ss_pred             HHHHHHHHHhccc
Q 040338          368 AELVMRNLLQLDV  380 (385)
Q Consensus       368 a~~~~~~~~~~~~  380 (385)
                      |...++-|...+.
T Consensus       580 A~~~lQ~a~~~n~  592 (625)
T KOG4422|consen  580 AIEVLQLASAFNL  592 (625)
T ss_pred             HHHHHHHHHHcCc
Confidence            9988888865543

>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=99.74  E-value=3.5e-15  Score=143.20  Aligned_cols=342  Identities=10%  Similarity=-0.018  Sum_probs=240.1

Q ss_pred             hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHH
Q 040338           33 LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF  110 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~  110 (385)
                      ++++|...|++..  .|+...|..+-.++..   .|++++|++.++...+.. +.+...|..+..+|...|++++|+.-|
T Consensus       142 ~~~~Ai~~y~~al~~~p~~~~~~n~a~~~~~---l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~lg~~~eA~~~~  217 (615)
T TIGR00990       142 DFNKAIKLYSKAIECKPDPVYYSNRAACHNA---LGDWEKVVEDTTAALELD-PDYSKALNRRANAYDGLGKYADALLDL  217 (615)
T ss_pred             CHHHHHHHHHHHHhcCCchHHHHHHHHHHHH---hCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            8888888888765  6777777777777666   899999999999988764 335678888889999999999998766


Q ss_pred             HhccCCCccccc------------cchHHHHHHhcCCCCCCcchHHHH------------------------------HH
Q 040338          111 LRMLNPSLFCWK------------FGIIRLLIMFQKMPERDLVSWNTM------------------------------IS  148 (385)
Q Consensus       111 ~~m~~~~~~~~~------------~~~~~a~~~~~~~~~~~~~~~~~l------------------------------i~  148 (385)
                      ......+.+...            .....+...+..-+ ++...+..+                              +.
T Consensus       218 ~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (615)
T TIGR00990       218 TASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKP-ENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEETGNGQLQ  296 (615)
T ss_pred             HHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHHccCCcchhhhhcccccccccccchHH
Confidence            554322211000            00011111111111 110000000                              00


Q ss_pred             HH------HhCCCchHHHHHHHHHHHCC-CCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          149 IL------TRHGFGFETLCTFIELWNHG-FGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       149 ~~------~~~~~~~~a~~~~~~m~~~g-~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      ..      ...+++++|.+.|++..+.+ ..| +...+..+...+...|++++|+..++..+...+ .....|..+...+
T Consensus       297 l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P-~~~~~~~~la~~~  375 (615)
T TIGR00990       297 LGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDP-RVTQSYIKRASMN  375 (615)
T ss_pred             HHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CcHHHHHHHHHHH
Confidence            00      12356778888888877654 334 345566667777778888888888888776532 2344666666667


Q ss_pred             HhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHH
Q 040338          221 LKCGCNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFF  285 (385)
Q Consensus       221 ~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~  285 (385)
                      ...|+++            .+.+..+|..+...+...|++++|+..|++..+  | +...+..+...+.+.|++++|+..
T Consensus       376 ~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~  455 (615)
T TIGR00990       376 LELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMAT  455 (615)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            7766655            344567888899999999999999999998876  3 556777888899999999999999


Q ss_pred             H------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--h-------hhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          286 F------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T-------CYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       286 ~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~-------~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      +            .++.+...+...|++++|...|++.....+  .       ..++.....+...|++++|.+++++..
T Consensus       456 ~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl  535 (615)
T TIGR00990       456 FRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKAL  535 (615)
T ss_pred             HHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            8            788899999999999999999999887654  1       112222333445799999999999875


Q ss_pred             CC-CC-cchHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          345 SK-PT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       345 ~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      .. |+ ...+..+...+...|++++|+..|++..+...
T Consensus       536 ~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l~~  573 (615)
T TIGR00990       536 IIDPECDIAVATMAQLLLQQGDVDEALKLFERAAELAR  573 (615)
T ss_pred             hcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhc
Confidence            53 44 44688899999999999999999999876543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.72  E-value=7.9e-15  Score=124.93  Aligned_cols=303  Identities=14%  Similarity=0.097  Sum_probs=235.2

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh--cCChhHH-HHHHHhccCCC---ccccc
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK--CGAVDYA-ESAFLRMLNPS---LFCWK  122 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~--~g~~~~a-~~~~~~m~~~~---~~~~~  122 (385)
                      +.+=|.|+...+    .|.++.+.-+++.|.+.|++.+..+--.|++.-+-  ..++--| ++-|-.|.+.+   ..+|.
T Consensus       116 V~~E~nL~kmIS----~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK  191 (625)
T KOG4422|consen  116 VETENNLLKMIS----SREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWK  191 (625)
T ss_pred             hcchhHHHHHHh----hcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccc
Confidence            445677776544    49999999999999999999888887777764443  3333322 45566676544   34565


Q ss_pred             -cchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHH
Q 040338          123 -FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRV  201 (385)
Q Consensus       123 -~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  201 (385)
                       |++.+   ++-+..+.+..+|.++|.++|+.-..+.|.++|.+-.....+.+..+||.+|.+-+-    ....++..+|
T Consensus       192 ~G~vAd---L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~----~~~K~Lv~EM  264 (625)
T KOG4422|consen  192 SGAVAD---LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSY----SVGKKLVAEM  264 (625)
T ss_pred             cccHHH---HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHh----hccHHHHHHH
Confidence             66654   555555677789999999999999999999999999988889999999999887543    2337899999


Q ss_pred             HHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----CChhhHHHHHHHHHhcC
Q 040338          202 VHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR----RNMISWMVLISAFSQAG  277 (385)
Q Consensus       202 ~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~li~~~~~~g  277 (385)
                      ......||..|+|+++.+..+.|++..                  ....|.+++.+|++    |...+|..+|..+++.+
T Consensus       265 isqkm~Pnl~TfNalL~c~akfg~F~~------------------ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~  326 (625)
T KOG4422|consen  265 ISQKMTPNLFTFNALLSCAAKFGKFED------------------ARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRES  326 (625)
T ss_pred             HHhhcCCchHhHHHHHHHHHHhcchHH------------------HHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccC
Confidence            999998888888666666555552210                  12345667777775    78889999999999988


Q ss_pred             CCCchHHHH----------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc----------hhhHHHHHH
Q 040338          278 VLEKPRFFF----------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----------TCYFVCMVD  325 (385)
Q Consensus       278 ~~~~a~~~~----------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----------~~~~~~li~  325 (385)
                      +..+....|                      .|...++.|.+..+.+.|.++..-......          ...|..+..
T Consensus       327 dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~  406 (625)
T KOG4422|consen  327 DPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFD  406 (625)
T ss_pred             CchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHH
Confidence            887755555                      788889999999999999998876654332          455677888


Q ss_pred             HHHccCCHHHHHHHHHhCCCC---CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          326 LLGLSGLLGEAKKLIDEMPSK---PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       326 ~~~~~g~~~~A~~~~~~m~~~---p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      ..|+....+.-.+.|+.|..+   |+..+-..++++....|.++-.-+++.+++..|.
T Consensus       407 licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~gh  464 (625)
T KOG4422|consen  407 LICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGH  464 (625)
T ss_pred             HHHHHHHHHHHHHHHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhh
Confidence            999999999999999999986   8999999999999999999999999999988773

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.72  E-value=1.6e-14  Score=138.55  Aligned_cols=296  Identities=11%  Similarity=-0.045  Sum_probs=233.3

Q ss_pred             cccCCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHhhhC--CC-ChhhHHHHHHHHHhhhccCChHH
Q 040338            4 CGSLKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFCDIG--PR-YLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      +-+.|+++.|+.+.+.++.....+.-..+          ++++|...|+++.  .| +...|..+...+..   .|++++
T Consensus        52 ~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~---~g~~~~  128 (656)
T PRK15174         52 CLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLK---SKQYAT  128 (656)
T ss_pred             HHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH---cCCHHH
Confidence            45789999999999999988766654444          9999999999886  34 44566666666556   899999


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHH
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISIL  150 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  150 (385)
                      |...++...+.. +.+...+..+..++...|+.++|...++++....+                   .+...+..+ ..+
T Consensus       129 Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P-------------------~~~~a~~~~-~~l  187 (656)
T PRK15174        129 VADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVP-------------------PRGDMIATC-LSF  187 (656)
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCC-------------------CCHHHHHHH-HHH
Confidence            999999999863 34577888999999999999999999988755442                   233344333 347


Q ss_pred             HhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCc
Q 040338          151 TRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIES  230 (385)
Q Consensus       151 ~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~  230 (385)
                      .+.|++++|...++.+.+....++...+..+..++.+.|++++|+..++...+..+. +                     
T Consensus       188 ~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~-~---------------------  245 (656)
T PRK15174        188 LNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLD-G---------------------  245 (656)
T ss_pred             HHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-C---------------------
Confidence            889999999999999877643345555566677888999999999999999886532 2                     


Q ss_pred             hhhHHHHHHHHHHcCCChhH----HHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHH
Q 040338          231 SIQIGKALVTMYAEGGSTQK----ADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSL  291 (385)
Q Consensus       231 ~~~~~~~li~~~~~~g~~~~----A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l  291 (385)
                       ...+..+...+...|++++    |+..|++..+  | +...+..+...+...|++++|+..+            .+..+
T Consensus       246 -~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~L  324 (656)
T PRK15174        246 -AALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMY  324 (656)
T ss_pred             -HHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence             2334566677777778875    7888888765  4 5568888899999999999999888            67778


Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  346 (385)
                      ..++...|++++|...++.+....+  ...+..+..++...|+.++|.+.|++..+.
T Consensus       325 a~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        325 ARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            8899999999999999999998777  344445677889999999999999988663

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.71  E-value=3.3e-14  Score=145.30  Aligned_cols=335  Identities=8%  Similarity=-0.059  Sum_probs=250.1

Q ss_pred             cccCCChHHHHHHHHHHHHcccchhh---H------------H-------h--hhhhHHHHHhhhC--C-CChhhHHHHH
Q 040338            4 CGSLKSLPIARKIHAQLISTCLISSI---F------------L-------Q--LIDDDYRVFCDIG--P-RYLFTYNTMI   56 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~~~~---~------------~-------~--~~~~A~~~~~~~~--~-~~~~~~~~li   56 (385)
                      +.+.|++++|+..++++.+.......   +            .       .  ++++|...|++..  . .+...+..+-
T Consensus       313 ~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg  392 (1157)
T PRK11447        313 YSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLG  392 (1157)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            45789999999999999986543211   0            0       0  8899999999876  2 3445566666


Q ss_pred             HHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc------------------
Q 040338           57 NGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL------------------  118 (385)
Q Consensus        57 ~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~------------------  118 (385)
                      ..+..   .|++++|++.|++..+.. +.+...+..+...|. .++.++|..+++.+.....                  
T Consensus       393 ~~~~~---~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~-~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~  467 (1157)
T PRK11447        393 DVAMA---RKDYAAAERYYQQALRMD-PGNTNAVRGLANLYR-QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQ  467 (1157)
T ss_pred             HHHHH---CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH-hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHH
Confidence            66656   899999999999999864 335566777777774 4678999988877643211                  


Q ss_pred             ---cccccchHHHHHHhcCCC--CC-CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCc
Q 040338          119 ---FCWKFGIIRLLIMFQKMP--ER-DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDL  191 (385)
Q Consensus       119 ---~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~  191 (385)
                         ....|+.++|+..|++..  .| +...+..+...|.+.|++++|...|++..+.  .| +...+..+...+...++.
T Consensus       468 a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~--~P~~~~~~~a~al~l~~~~~~  545 (1157)
T PRK11447        468 AEALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQ--KPNDPEQVYAYGLYLSGSDRD  545 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHhCCCH
Confidence               111288899999888764  23 4567778889999999999999999999874  34 344444444556778999


Q ss_pred             cchhhHHHHHHHhCCCCchH---------HHHHHHHHHHhcCCCC--------CCchhhHHHHHHHHHHcCCChhHHHHH
Q 040338          192 EWGPHLHSRVVHMEPSLDVF---------VGSGLIDMYLKCGCNG--------IESSIQIGKALVTMYAEGGSTQKADLA  254 (385)
Q Consensus       192 ~~a~~~~~~~~~~~~~~~~~---------~~~~li~~~~~~g~~~--------~~~~~~~~~~li~~~~~~g~~~~A~~~  254 (385)
                      ++|...++.+......++..         .+..+...+...|+.+        .+.+...+..+...+.+.|+.++|+..
T Consensus       546 ~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~  625 (1157)
T PRK11447        546 RAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAA  625 (1157)
T ss_pred             HHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHH
Confidence            99999888765433222211         1223345555666544        445666778899999999999999999


Q ss_pred             HHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--h
Q 040338          255 FELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T  317 (385)
Q Consensus       255 ~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~  317 (385)
                      |++..+  | +...+..++..|...|++++|++.+            .+..+..++...|++++|.++++.+.....  .
T Consensus       626 y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~  705 (1157)
T PRK11447        626 YQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQP  705 (1157)
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCC
Confidence            998876  3 6788899999999999999999998            566677888899999999999999887644  1


Q ss_pred             ------hhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          318 ------CYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       318 ------~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                            ..+..+...+...|++++|+..|+....
T Consensus       706 ~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        706 PSMESALVLRDAARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             cchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence                  3455567888999999999999998764

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

Probab=99.71  E-value=2.1e-15  Score=133.97  Aligned_cols=330  Identities=12%  Similarity=0.037  Sum_probs=236.1

Q ss_pred             cCCChHHHHHHHHHHHHcccchhhHHh------------hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHH
Q 040338            6 SLKSLPIARKIHAQLISTCLISSIFLQ------------LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMA   71 (385)
Q Consensus         6 ~~~~~~~a~~~~~~~~~~~~~~~~~~~------------~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a   71 (385)
                      ..|+++.|......+++..  |...-.            +.+.|...|.+..  .|+.....+-+..+.+.  .|++.+|
T Consensus       128 erg~~~~al~~y~~aiel~--p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnLlka--~Grl~ea  203 (966)
T KOG4626|consen  128 ERGQLQDALALYRAAIELK--PKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNLLKA--EGRLEEA  203 (966)
T ss_pred             HhchHHHHHHHHHHHHhcC--chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHHHHh--hcccchh
Confidence            4567777777777777642  211111            6666666665544  33333322222222221  5666666


Q ss_pred             HHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccc------------cchHHHHHHhcC---CC
Q 040338           72 LHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK------------FGIIRLLIMFQK---MP  136 (385)
Q Consensus        72 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~------------~~~~~a~~~~~~---~~  136 (385)
                      ...+.+.++... --...|+.|...+-..|++-.|+.-|++..+.++.--.            +.+++|..-+.+   +.
T Consensus       204 ~~cYlkAi~~qp-~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lr  282 (966)
T KOG4626|consen  204 KACYLKAIETQP-CFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVYKEARIFDRAVSCYLRALNLR  282 (966)
T ss_pred             HHHHHHHHhhCC-ceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhcC
Confidence            666666665421 12345666666666666666666666666554431100            333333333222   12


Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                      +....+|..+...|-..|..+-|++.|++..+  +.|+ ...|+.|.+++-..|++.+|.+.+...+...+         
T Consensus       283 pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~--~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p---------  351 (966)
T KOG4626|consen  283 PNHAVAHGNLACIYYEQGLLDLAIDTYKRALE--LQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCP---------  351 (966)
T ss_pred             CcchhhccceEEEEeccccHHHHHHHHHHHHh--cCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCC---------
Confidence            34566777888889999999999999999987  4665 67899999999999999999999999988643         


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CC-hhhHHHHHHHHHhcCCCCchHHHH------
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RN-MISWMVLISAFSQAGVLEKPRFFF------  286 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~g~~~~a~~~~------  286 (385)
                                    ....+.+.|...|...|++++|..+|....+  |+ ...++.|...|-++|++++|+..+      
T Consensus       352 --------------~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI  417 (966)
T KOG4626|consen  352 --------------NHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRI  417 (966)
T ss_pred             --------------ccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhc
Confidence                          2334567888999999999999999998876  43 367889999999999999999888      


Q ss_pred             ------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCCc-chHHHHH
Q 040338          287 ------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPTC-VIWGALL  356 (385)
Q Consensus       287 ------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~~-~~~~~li  356 (385)
                            +|+.+...|...|+++.|.+.+.+....++  ...++-|...|-.+|++.+|+.-|++... +||. ..|..++
T Consensus       418 ~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkPDfpdA~cNll  497 (966)
T KOG4626|consen  418 KPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKPDFPDAYCNLL  497 (966)
T ss_pred             CchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCCCCchhhhHHH
Confidence                  899999999999999999999999999998  88899999999999999999999998876 4664 3566777


Q ss_pred             HHHHhcCCh
Q 040338          357 GACCSHYNT  365 (385)
Q Consensus       357 ~~~~~~g~~  365 (385)
                      .+..--.++
T Consensus       498 h~lq~vcdw  506 (966)
T KOG4626|consen  498 HCLQIVCDW  506 (966)
T ss_pred             HHHHHHhcc
Confidence            665444444

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.70  E-value=6.2e-14  Score=137.20  Aligned_cols=353  Identities=8%  Similarity=-0.112  Sum_probs=235.4

Q ss_pred             cccCCChHHHHHHHHHHHHcc-cchhhHHh---------hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHH
Q 040338            4 CGSLKSLPIARKIHAQLISTC-LISSIFLQ---------LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~---------~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      ....|+.++|..++....... ........         ++++|..+|++..   +.+...+..+...+..   .|++++
T Consensus        25 a~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~---~g~~~e  101 (765)
T PRK10049         25 ALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLAD---AGQYDE  101 (765)
T ss_pred             HHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH---CCCHHH
Confidence            456799999999999988633 33211111         8999999999854   3345556666666666   899999


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccc------------cchHHHHHHhcCCCC-
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK------------FGIIRLLIMFQKMPE-  137 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~------------~~~~~a~~~~~~~~~-  137 (385)
                      |...+++..+.. +.+.. +..+..++...|+.++|+..++++.+..+-...            +..+.|+..++.... 
T Consensus       102 A~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~  179 (765)
T PRK10049        102 ALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDANLT  179 (765)
T ss_pred             HHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCCC
Confidence            999999998873 34556 888888999999999999999998765531111            444555555554433 


Q ss_pred             CCc------chHHHHHHHHH-----hCCCc---hHHHHHHHHHHHC-CCCCCHh-hHH----HHHHHhcCccCccchhhH
Q 040338          138 RDL------VSWNTMISILT-----RHGFG---FETLCTFIELWNH-GFGLSSM-LYA----TAFSARASVYDLEWGPHL  197 (385)
Q Consensus       138 ~~~------~~~~~li~~~~-----~~~~~---~~a~~~~~~m~~~-g~~p~~~-t~~----~ll~~~~~~~~~~~a~~~  197 (385)
                      |+.      .....++....     ..+++   ++|+..++.+.+. ...|+.. .+.    ..+.++...|+.++|+..
T Consensus       180 p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~  259 (765)
T PRK10049        180 PAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISE  259 (765)
T ss_pred             HHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            110      01111121111     11222   4566666666543 1222211 111    112233455666777777


Q ss_pred             HHHHHHhCCC-CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCC-------hhhHHHH
Q 040338          198 HSRVVHMEPS-LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRN-------MISWMVL  269 (385)
Q Consensus       198 ~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~-------~~~~~~l  269 (385)
                      |+.+.+.+.. |+..                     .  ..+...|...|++++|+..|+.+.+.+       ......+
T Consensus       260 ~~~ll~~~~~~P~~a---------------------~--~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L  316 (765)
T PRK10049        260 YQRLKAEGQIIPPWA---------------------Q--RWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADL  316 (765)
T ss_pred             HHHhhccCCCCCHHH---------------------H--HHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHH
Confidence            7776665431 2211                     1  113556777788888888888775422       1234556


Q ss_pred             HHHHHhcCCCCchHHHH---------------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhH
Q 040338          270 ISAFSQAGVLEKPRFFF---------------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYF  320 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~---------------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~  320 (385)
                      ..++...|++++|.+.+                           .+..+...+...|+.++|+++++++....+  ...+
T Consensus       317 ~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~  396 (765)
T PRK10049        317 FYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLR  396 (765)
T ss_pred             HHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHH
Confidence            66777888888888776                           123456677889999999999999988877  8888


Q ss_pred             HHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHHHHHhcCChHHHHHHHHHHHhccccCCC
Q 040338          321 VCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       321 ~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      ..+...+...|++++|++.+++.... |+ ...+...+..+...|++++|..+++++++..|.++.
T Consensus       397 ~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~~~  462 (765)
T PRK10049        397 IDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQDPG  462 (765)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCHH
Confidence            88999999999999999999998874 65 456667777899999999999999999998887653

>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=99.66  E-value=2e-13  Score=131.06  Aligned_cols=297  Identities=11%  Similarity=-0.017  Sum_probs=217.4

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|+..|++.++.  .|+...|..+..+|.+.|++++|++.++...+.+                   +.+...|.
T Consensus       140 ~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-------------------p~~~~a~~  198 (615)
T TIGR00990       140 NKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-------------------PDYSKALN  198 (615)
T ss_pred             cCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-------------------CCCHHHHH
Confidence            89999999999999874  6788889999999999999999999998887655                   34566788


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCC----------------------------CCC-C---HhhHHHHHHH--------
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHG----------------------------FGL-S---SMLYATAFSA--------  184 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g----------------------------~~p-~---~~t~~~ll~~--------  184 (385)
                      .+..+|...|++++|+.-|......+                            ..| +   ..........        
T Consensus       199 ~~a~a~~~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (615)
T TIGR00990       199 RRANAYDGLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPA  278 (615)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchh
Confidence            88888888888888876554432211                            011 0   0000000000        


Q ss_pred             -------------------------hcCccCccchhhHHHHHHHhC-CCC-chHHHHHHHHHHHhcCCCC----------
Q 040338          185 -------------------------RASVYDLEWGPHLHSRVVHME-PSL-DVFVGSGLIDMYLKCGCNG----------  227 (385)
Q Consensus       185 -------------------------~~~~~~~~~a~~~~~~~~~~~-~~~-~~~~~~~li~~~~~~g~~~----------  227 (385)
                                               ....+++++|.+.|+...+.+ ..| ....+..+...+...|+.+          
T Consensus       279 ~~~~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal  358 (615)
T TIGR00990       279 GLEDSNELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSI  358 (615)
T ss_pred             hhhcccccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence                                     011246778888888888765 223 3456777777777777766          


Q ss_pred             -CCch-hhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHH
Q 040338          228 -IESS-IQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVS  290 (385)
Q Consensus       228 -~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~  290 (385)
                       ..|+ ...|..+...+...|++++|+..|++..+  | +...|..+...+...|++++|+..+            .+..
T Consensus       359 ~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~  438 (615)
T TIGR00990       359 ELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQ  438 (615)
T ss_pred             HcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHH
Confidence             3444 56788888888899999999999988765  2 5678888888899999999999888            6777


Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCc-ch-------HHHHHHHH
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTC-VI-------WGALLGAC  359 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~-~~-------~~~li~~~  359 (385)
                      +...+.+.|++++|...+++..+..+  ...++.+...+...|++++|++.|+..... |+. ..       ++..+..+
T Consensus       439 la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~  518 (615)
T TIGR00990       439 LGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALF  518 (615)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHH
Confidence            78888889999999999999887766  778888888999999999999999886652 321 11       12222234


Q ss_pred             HhcCChHHHHHHHHHHHhccccC
Q 040338          360 CSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       360 ~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ...|++++|.+++++.++.+|.+
T Consensus       519 ~~~~~~~eA~~~~~kAl~l~p~~  541 (615)
T TIGR00990       519 QWKQDFIEAENLCEKALIIDPEC  541 (615)
T ss_pred             HHhhhHHHHHHHHHHHHhcCCCc
Confidence            44689999999999988877654

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.66  E-value=1.4e-12  Score=126.03  Aligned_cols=354  Identities=11%  Similarity=-0.032  Sum_probs=207.1

Q ss_pred             ccCCChHHHHHHHHHHHHcccchh-h-----HHh----hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHH
Q 040338            5 GSLKSLPIARKIHAQLISTCLISS-I-----FLQ----LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHL   74 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~~~~-~-----~~~----~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~   74 (385)
                      .+.|++..|+..+.++.+...... .     .+.    +.++|...+++...|+...+..+......+...|++++|+++
T Consensus        45 ~r~Gd~~~Al~~L~qaL~~~P~~~~av~dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiel  124 (822)
T PRK14574         45 ARAGDTAPVLDYLQEESKAGPLQSGQVDDWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALAL  124 (822)
T ss_pred             HhCCCHHHHHHHHHHHHhhCccchhhHHHHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            578999999999999998765532 1     111    899999999988877666655555332223337999999999


Q ss_pred             HHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCC
Q 040338           75 HGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHG  154 (385)
Q Consensus        75 ~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~  154 (385)
                      ++++.+... -++..+..++..+.+.++.++|++.++++.+.+                    |+...+-.++..+...+
T Consensus       125 y~kaL~~dP-~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~d--------------------p~~~~~l~layL~~~~~  183 (822)
T PRK14574        125 WQSSLKKDP-TNPDLISGMIMTQADAGRGGVVLKQATELAERD--------------------PTVQNYMTLSYLNRATD  183 (822)
T ss_pred             HHHHHhhCC-CCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccC--------------------cchHHHHHHHHHHHhcc
Confidence            999998753 356777788899999999999999999887655                    44444544444444456


Q ss_pred             CchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHH--------------------HhCCCCch---
Q 040338          155 FGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVV--------------------HMEPSLDV---  210 (385)
Q Consensus       155 ~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~--------------------~~~~~~~~---  210 (385)
                      +..+|+..++++.+.  .| +...+..+..++.+.|-...|.++..+-.                    +.+..++.   
T Consensus       184 ~~~~AL~~~ekll~~--~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~  261 (822)
T PRK14574        184 RNYDALQASSEAVRL--APTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSET  261 (822)
T ss_pred             hHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccch
Confidence            665688888888775  45 45555666667776666555554433211                    11110100   


Q ss_pred             HHHHHHHHHHHhcC----CCC-CCch----hhHHHHHHHHHHcCCChhHHHHHHHhcccC--Chh--hHHHHHHHHHhcC
Q 040338          211 FVGSGLIDMYLKCG----CNG-IESS----IQIGKALVTMYAEGGSTQKADLAFELMSRR--NMI--SWMVLISAFSQAG  277 (385)
Q Consensus       211 ~~~~~li~~~~~~g----~~~-~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~--~~~~li~~~~~~g  277 (385)
                      .-|..+=.++....    ... .++.    ..+.-=.+-++...|++.++++.|+.|+.+  .+.  +-..+.++|...+
T Consensus       262 ~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~  341 (822)
T PRK14574        262 ERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRR  341 (822)
T ss_pred             hhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcC
Confidence            00000000111000    000 1111    111122344555566666666666666642  122  3334566666666


Q ss_pred             CCCchHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-----------------hhhHHH
Q 040338          278 VLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----------------TCYFVC  322 (385)
Q Consensus       278 ~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------------~~~~~~  322 (385)
                      ++++|+.++                  ....|.-++...+++++|.++++.+.+..+                 ...+..
T Consensus       342 ~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l  421 (822)
T PRK14574        342 LPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTL  421 (822)
T ss_pred             CcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHH
Confidence            666666666                  023456666666666666666666665222                 223334


Q ss_pred             HHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          323 MVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       323 li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ++..+...|++.+|++.++++... | |......+...+...|.+.+|.+.++......|.
T Consensus       422 ~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~  482 (822)
T PRK14574        422 LVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVESLAPR  482 (822)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCc
Confidence            555566666666666666666543 2 4455555666666666666666666655555544

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.62  E-value=8.8e-13  Score=129.19  Aligned_cols=322  Identities=8%  Similarity=-0.055  Sum_probs=233.7

Q ss_pred             hhhhHHHHHhhhCC---CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIGP---RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      +.++|..++.+..+   .+...+..+...+..   .|++++|..++++..+.. +.+...+..+..++.+.|+.++|...
T Consensus        30 ~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~---~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g~~~eA~~~  105 (765)
T PRK10049         30 QDAEVITVYNRYRVHMQLPARGYAAVAVAYRN---LKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAGQYDEALVK  105 (765)
T ss_pred             CHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            89999999988763   233447777777666   899999999999998863 44567778888999999999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCc
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASV  188 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~  188 (385)
                      +++..+..                   +.+.. +..+...+...|++++|+..++++.+.  .| +...+..+..++...
T Consensus       106 l~~~l~~~-------------------P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~--~P~~~~~~~~la~~l~~~  163 (765)
T PRK10049        106 AKQLVSGA-------------------PDKAN-LLALAYVYKRAGRHWDELRAMTQALPR--APQTQQYPTEYVQALRNN  163 (765)
T ss_pred             HHHHHHhC-------------------CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHC
Confidence            99987665                   34555 888888999999999999999999885  45 444555667777778


Q ss_pred             cCccchhhHHHHHHHhCCCCch------HH------------------H---HHHHH---HHHhc--CCCCCCchh-hHH
Q 040338          189 YDLEWGPHLHSRVVHMEPSLDV------FV------------------G---SGLID---MYLKC--GCNGIESSI-QIG  235 (385)
Q Consensus       189 ~~~~~a~~~~~~~~~~~~~~~~------~~------------------~---~~li~---~~~~~--g~~~~~~~~-~~~  235 (385)
                      +..+.|++.++....   .|+.      ..                  +   ..-+.   .+.+.  .+++..|.. ...
T Consensus       164 ~~~e~Al~~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~  240 (765)
T PRK10049        164 RLSAPALGAIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRAR  240 (765)
T ss_pred             CChHHHHHHHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHH
Confidence            888888877775443   1110      00                  0   00011   11111  111111111 111


Q ss_pred             HHHHHHHHcCCChhHHHHHHHhcccCC--hh--hHHHHHHHHHhcCCCCchHHHH----------------HHHHHHHHh
Q 040338          236 KALVTMYAEGGSTQKADLAFELMSRRN--MI--SWMVLISAFSQAGVLEKPRFFF----------------FFVSLLSGC  295 (385)
Q Consensus       236 ~~li~~~~~~g~~~~A~~~~~~m~~~~--~~--~~~~li~~~~~~g~~~~a~~~~----------------~~~~l~~~~  295 (385)
                      ...+..+...|++++|+..|+.+.+.+  ..  .-..+..+|...|++++|+..+                ....+..++
T Consensus       241 ~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~  320 (765)
T PRK10049        241 IDRLGALLARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSL  320 (765)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHH
Confidence            111334567799999999999998742  12  2233577899999999999998                133455578


Q ss_pred             cccCChhhHHHHHHHHHhccc-----------------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY-----------------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALL  356 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~-----------------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li  356 (385)
                      ...|++++|.+.++.+....+                 ...+..+...+...|+.++|+++++++... | +...+..+.
T Consensus       321 ~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA  400 (765)
T PRK10049        321 LESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYA  400 (765)
T ss_pred             HhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            899999999999999988643                 123456777889999999999999998774 4 566788999


Q ss_pred             HHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          357 GACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ..+...|++++|++.+++..+..|.+.
T Consensus       401 ~l~~~~g~~~~A~~~l~~al~l~Pd~~  427 (765)
T PRK10049        401 SVLQARGWPRAAENELKKAEVLEPRNI  427 (765)
T ss_pred             HHHHhcCCHHHHHHHHHHHHhhCCCCh
Confidence            999999999999999999999988753

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.61  E-value=3e-12  Score=123.80  Aligned_cols=325  Identities=10%  Similarity=-0.083  Sum_probs=223.7

Q ss_pred             hhhhHHHHHhhhC--CCChh-hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG--PRYLF-TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~-~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|...|++..  .|+.. ....++..+..   .|+.++|+..+++.... -+........+...|...|++++|.++
T Consensus        49 d~~~Al~~L~qaL~~~P~~~~av~dll~l~~~---~G~~~~A~~~~eka~~p-~n~~~~~llalA~ly~~~gdyd~Aiel  124 (822)
T PRK14574         49 DTAPVLDYLQEESKAGPLQSGQVDDWLQIAGW---AGRDQEVIDVYERYQSS-MNISSRGLASAARAYRNEKRWDQALAL  124 (822)
T ss_pred             CHHHHHHHHHHHHhhCccchhhHHHHHHHHHH---cCCcHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            7778888888776  33321 12256666555   78888888888888721 111222233335577777888888888


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY  189 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~  189 (385)
                      |+++.+.+                   +.|...+..++..+...++.++|++.++++...  .|+...+..++..+...+
T Consensus       125 y~kaL~~d-------------------P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~  183 (822)
T PRK14574        125 WQSSLKKD-------------------PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATD  183 (822)
T ss_pred             HHHHHhhC-------------------CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcc
Confidence            88887766                   345667778889999999999999999999775  667666655555554566


Q ss_pred             CccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC-------CCch-----hhHH------HHHHHHH-----HcCC
Q 040338          190 DLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG-------IESS-----IQIG------KALVTMY-----AEGG  246 (385)
Q Consensus       190 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~-------~~~~-----~~~~------~~li~~~-----~~~g  246 (385)
                      +..+|++.++++.+.. +-+...+..++.++.+.|-..       ..|+     ...+      ..+++.-     ....
T Consensus       184 ~~~~AL~~~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~  262 (822)
T PRK14574        184 RNYDALQASSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETE  262 (822)
T ss_pred             hHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchh
Confidence            6666999999999985 346677788888888888554       1111     1000      0111100     0111


Q ss_pred             C---hhHHHHHHHhccc-----CCh-hhHH----HHHHHHHhcCCCCchHHHH-------------HHHHHHHHhcccCC
Q 040338          247 S---TQKADLAFELMSR-----RNM-ISWM----VLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGP  300 (385)
Q Consensus       247 ~---~~~A~~~~~~m~~-----~~~-~~~~----~li~~~~~~g~~~~a~~~~-------------~~~~l~~~~~~~~~  300 (385)
                      +   .+.|+.-++.+..     |.. ..|.    -.+-++...|+..++++.+             +-..+.++|...+.
T Consensus       263 r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~  342 (822)
T PRK14574        263 RFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRL  342 (822)
T ss_pred             hHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCC
Confidence            2   3345555555443     211 1221    2355677888999998888             67789999999999


Q ss_pred             hhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC---------------c-chHHHH
Q 040338          301 VTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT---------------C-VIWGAL  355 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~---------------~-~~~~~l  355 (385)
                      +++|..+++.+.....        ......|.-+|..++++++|..+++.+.+. |.               - ..+..+
T Consensus       343 P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~  422 (822)
T PRK14574        343 PEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLL  422 (822)
T ss_pred             cHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHH
Confidence            9999999999876542        222467899999999999999999999873 31               1 124456


Q ss_pred             HHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          356 LGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       356 i~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +..+.-.|+.++|.+.++++....|.+.
T Consensus       423 a~~~~~~gdl~~Ae~~le~l~~~aP~n~  450 (822)
T PRK14574        423 VQSLVALNDLPTAQKKLEDLSSTAPANQ  450 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCH
Confidence            7888999999999999999999888764

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.59  E-value=8.1e-12  Score=123.25  Aligned_cols=159  Identities=11%  Similarity=-0.020  Sum_probs=97.0

Q ss_pred             cccCCChHHHHHHHHHHHHcccchhhHHh-------hhhhHHHHHhhhC--CCC-hhhHHHHHHHH-----HhhhccCCh
Q 040338            4 CGSLKSLPIARKIHAQLISTCLISSIFLQ-------LIDDDYRVFCDIG--PRY-LFTYNTMINGG-----VRCLCVGNI   68 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-------~~~~A~~~~~~~~--~~~-~~~~~~li~~~-----~~~~~~~~~   68 (385)
                      +.+.|++++|+...+..++.... +....       +.++|..+++++.  .|+ ...+..+....     ..   -.+.
T Consensus        88 yl~~g~~~~A~~~~~kAv~ldP~-n~~~~~~La~i~~~~kA~~~ye~l~~~~P~n~~~~~~la~~~~~~~~l~---y~q~  163 (987)
T PRK09782         88 YRHFGHDDRARLLLEDQLKRHPG-DARLERSLAAIPVEVKSVTTVEELLAQQKACDAVPTLRCRSEVGQNALR---LAQL  163 (987)
T ss_pred             HHHCCCHHHHHHHHHHHHhcCcc-cHHHHHHHHHhccChhHHHHHHHHHHhCCCChhHHHHHHHHhhccchhh---hhhH
Confidence            44566777777777776665431 11111       6667777777665  333 22222222220     01   1333


Q ss_pred             HHHHHHHHHHHHhccCCCchHHHhH-HHHHHhcCChhHHHHHHHhccCCCccccc-------------cchHHHHHHhcC
Q 040338           69 KMALHLHGLVKKFYFVSDESIAKSS-IDMHVKCGAVDYAESAFLRMLNPSLFCWK-------------FGIIRLLIMFQK  134 (385)
Q Consensus        69 ~~a~~~~~~m~~~g~~~~~~~~~~l-i~~~~~~g~~~~a~~~~~~m~~~~~~~~~-------------~~~~~a~~~~~~  134 (385)
                      ++|.+.++ .......|+..+.... .+.|.+.|++++|++++.++.+.++....             +. +.+..++.+
T Consensus       164 eqAl~AL~-lr~~~~~~~~~vL~L~~~rlY~~l~dw~~Ai~lL~~L~k~~pl~~~~~~~L~~ay~q~l~~-~~a~al~~~  241 (987)
T PRK09782        164 PVARAQLN-DATFAASPEGKTLRTDLLQRAIYLKQWSQADTLYNEARQQNTLSAAERRQWFDVLLAGQLD-DRLLALQSQ  241 (987)
T ss_pred             HHHHHHHH-HhhhCCCCCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCH-HHHHHHhch
Confidence            55555555 3333334445555555 78888899999999999998877653332             22 566666665


Q ss_pred             CCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          135 MPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       135 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      ..+.++..+..+...|.+.|+.++|..+++++..
T Consensus       242 ~lk~d~~l~~ala~~yi~~G~~~~A~~~L~~~~~  275 (987)
T PRK09782        242 GIFTDPQSRITYATALAYRGEKARLQHYLIENKP  275 (987)
T ss_pred             hcccCHHHHHHHHHHHHHCCCHHHHHHHHHhCcc
Confidence            4455777888888999999999999988888643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.55  E-value=1.7e-11  Score=111.14  Aligned_cols=289  Identities=10%  Similarity=-0.042  Sum_probs=214.4

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhH-HHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSS-IDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l-i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ....+..|+.... .|+++.|.+......+.+  +++..+..+ ..+..+.|+.+.|...+.++.+..            
T Consensus        84 ~~~~~~~gl~a~~-eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~------------  148 (398)
T PRK10747         84 ARKQTEQALLKLA-EGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAELA------------  148 (398)
T ss_pred             HHHHHHHHHHHHh-CCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC------------
Confidence            3444555554421 599999998877655532  233333333 344477899999999999987643            


Q ss_pred             HHhcCCCCCCcchHH--HHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          130 IMFQKMPERDLVSWN--TMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                              |+...+-  .....+...|+++.|...++++.+.  .| +......+...|.+.|+++++.+++..+.+.+.
T Consensus       149 --------~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~--~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~  218 (398)
T PRK10747        149 --------DNDQLPVEITRVRIQLARNENHAARHGVDKLLEV--APRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHV  218 (398)
T ss_pred             --------CcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCC
Confidence                    4433222  3357888999999999999999886  45 567778889999999999999999999999876


Q ss_pred             CCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchH
Q 040338          207 SLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       207 ~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~  283 (385)
                      .++. ....+-              ..+|..++.......+.+...++++.+.+   .+......+..++...|+.++|.
T Consensus       219 ~~~~-~~~~l~--------------~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~  283 (398)
T PRK10747        219 GDEE-HRAMLE--------------QQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQ  283 (398)
T ss_pred             CCHH-HHHHHH--------------HHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHH
Confidence            5322 121110              01222333333444566777777777754   36677778888888889988888


Q ss_pred             HHH---------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcch
Q 040338          284 FFF---------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVI  351 (385)
Q Consensus       284 ~~~---------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~  351 (385)
                      ..+         .-..++.+....++.+++.+..+...+..+  +.....+...+.+.|++++|.+.|+...+. |+..+
T Consensus       284 ~~L~~~l~~~~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~  363 (398)
T PRK10747        284 QIILDGLKRQYDERLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYD  363 (398)
T ss_pred             HHHHHHHhcCCCHHHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHH
Confidence            888         222344555566999999999999888888  777889999999999999999999999885 99999


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          352 WGALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       352 ~~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      |..+...+.+.|+.++|.+.+++-...-
T Consensus       364 ~~~La~~~~~~g~~~~A~~~~~~~l~~~  391 (398)
T PRK10747        364 YAWLADALDRLHKPEEAAAMRRDGLMLT  391 (398)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence            9999999999999999999999986643

>PF13041 PPR_2: PPR repeat family

Probab=99.51  E-value=4.6e-14  Score=86.89  Aligned_cols=50  Identities=28%  Similarity=0.309  Sum_probs=47.6

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS  187 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  187 (385)
                      ||+.+||++|.+|++.|++++|+++|++|.+.|++||..||+.+|++|++
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            78999999999999999999999999999999999999999999999875

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.51  E-value=1.1e-11  Score=122.33  Aligned_cols=291  Identities=10%  Similarity=-0.008  Sum_probs=178.4

Q ss_pred             cCChHHHHHHHHHHHHh-c-cCCCchHHHhHHHHHHhcCCh---hHHHHHHHhccCCCccccccchHHHH---HHhcCCC
Q 040338           65 VGNIKMALHLHGLVKKF-Y-FVSDESIAKSSIDMHVKCGAV---DYAESAFLRMLNPSLFCWKFGIIRLL---IMFQKMP  136 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~-g-~~~~~~~~~~li~~~~~~g~~---~~a~~~~~~m~~~~~~~~~~~~~~a~---~~~~~~~  136 (385)
                      .|+.++|.++++..... + -.++....+-|+..|.+.+.+   .++..+-..+..++...|.|....+.   ..+....
T Consensus       389 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al  468 (987)
T PRK09782        389 NGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLL  468 (987)
T ss_pred             cccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhc
Confidence            67788888888777662 1 223444555777888887773   34444433344444444555443322   2222221


Q ss_pred             ---CC--CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchH
Q 040338          137 ---ER--DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVF  211 (385)
Q Consensus       137 ---~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  211 (385)
                         ++  +...|..+..++.. +++++|+..+.+....  .|+......+...+...|++++|...++.+....  |+..
T Consensus       469 ~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~--p~~~  543 (987)
T PRK09782        469 GDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLHD--MSNE  543 (987)
T ss_pred             ccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhccC--CCcH
Confidence               23  56678888888776 8899999988887764  4776554445555678999999999999875542  2222


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChh---hHHHHHHHHHhcCCCCchHHHH--
Q 040338          212 VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMI---SWMVLISAFSQAGVLEKPRFFF--  286 (385)
Q Consensus       212 ~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~---~~~~li~~~~~~g~~~~a~~~~--  286 (385)
                      .+                      ..+...+.+.|+.++|...++...+.+..   .+..+.......|++++|+..+  
T Consensus       544 a~----------------------~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~  601 (987)
T PRK09782        544 DL----------------------LAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTR  601 (987)
T ss_pred             HH----------------------HHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            23                      33344555566666666666665543221   2222222333446666666666  


Q ss_pred             ---------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHH
Q 040338          287 ---------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWG  353 (385)
Q Consensus       287 ---------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~  353 (385)
                               .+..+..++.+.|+.++|...+++.....+  ...+..+...+...|+.++|+..|++..+. | +...+.
T Consensus       602 AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~  681 (987)
T PRK09782        602 SLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDPALIR  681 (987)
T ss_pred             HHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence                     556666666667777777777777666666  556666666677777777777777666542 3 344566


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          354 ALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       354 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .+..++...|++++|...+++..+..|..
T Consensus       682 nLA~al~~lGd~~eA~~~l~~Al~l~P~~  710 (987)
T PRK09782        682 QLAYVNQRLDDMAATQHYARLVIDDIDNQ  710 (987)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcCCCC
Confidence            66677777777777777777776666554

>TIGR00540 hemY_coli hemY protein

Probab=99.48  E-value=2.4e-10  Score=104.15  Aligned_cols=290  Identities=10%  Similarity=-0.061  Sum_probs=194.3

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHH-HhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIA-KSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~-~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ..+..+..|+.. ...|+++.|.+.+....+.  .|+...+ -....++.+.|+.+.|.+.+.+..+...          
T Consensus        83 k~~~~~~~glla-~~~g~~~~A~~~l~~~~~~--~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p----------  149 (409)
T TIGR00540        83 KAQKQTEEALLK-LAEGDYAKAEKLIAKNADH--AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAG----------  149 (409)
T ss_pred             HHHHHHHHHHHH-HhCCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC----------
Confidence            345556666554 2379999999999887664  4554433 3345777788999999999988754321          


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                              .+.....-.....+...|+++.|...++++.+.  .| +......+...+...|+++++.+.+..+.+.+..
T Consensus       150 --------~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~--~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~  219 (409)
T TIGR00540       150 --------NDNILVEIARTRILLAQNELHAARHGVDKLLEM--APRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF  219 (409)
T ss_pred             --------cCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC
Confidence                    222233344577788899999999999999886  35 5567788899999999999999999999998754


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHH
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRF  284 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~  284 (385)
                      +.......-..++               ..++..-......+.....++...+   .+...+..+...+...|+.++|.+
T Consensus       220 ~~~~~~~l~~~a~---------------~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~  284 (409)
T TIGR00540       220 DDEEFADLEQKAE---------------IGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQE  284 (409)
T ss_pred             CHHHHHHHHHHHH---------------HHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHH
Confidence            3332211111111               1111111111223333334443332   244455555555555555555555


Q ss_pred             HH----------H----HHHHHHHhcccCChhhHHHHHHHHHhccc--h--hhHHHHHHHHHccCCHHHHHHHHHh--CC
Q 040338          285 FF----------F----FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T--CYFVCMVDLLGLSGLLGEAKKLIDE--MP  344 (385)
Q Consensus       285 ~~----------~----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~--~~~~~li~~~~~~g~~~~A~~~~~~--m~  344 (385)
                      .+          .    ...........++.+.+.+.++...+..+  +  ....++...+.+.|++++|.+.|+.  ..
T Consensus       285 ~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~  364 (409)
T TIGR00540       285 IIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAAC  364 (409)
T ss_pred             HHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHh
Confidence            55          0    11122222335677888899988888777  5  6677899999999999999999993  43


Q ss_pred             C-CCCcchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          345 S-KPTCVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       345 ~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      + .|+...+..+...+.+.|+.++|.+++++...
T Consensus       365 ~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       365 KEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             hcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3 59998899999999999999999999998643

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.

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

Probab=99.45  E-value=2.5e-11  Score=112.46  Aligned_cols=84  Identities=7%  Similarity=-0.030  Sum_probs=75.4

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      |+..+|.+++.+-.-+|+.+.|..++.+|++.|++.+.+-|-.|+-+   .++...++.++.-|...|+.|+..|+...+
T Consensus       202 ~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyv  278 (1088)
T KOG4318|consen  202 PTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYV  278 (1088)
T ss_pred             CChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHH
Confidence            78889999999999999999999999999999999999988887765   788888899999999999999999999888


Q ss_pred             HHHHhcC
Q 040338          218 DMYLKCG  224 (385)
Q Consensus       218 ~~~~~~g  224 (385)
                      -.+.++|
T Consensus       279 ip~l~N~  285 (1088)
T KOG4318|consen  279 IPQLSNG  285 (1088)
T ss_pred             Hhhhcch
Confidence            7777755

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.45  E-value=6.8e-11  Score=107.15  Aligned_cols=267  Identities=10%  Similarity=0.005  Sum_probs=191.7

Q ss_pred             hhhhHHHHHhhhCCC-ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHH--hHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIGPR-YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAK--SSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~--~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|.+.+...+.. +...-+.++.+.. ....|+++.|.+.+.++.+.  .|+...+.  .....+...|+.+.|...
T Consensus        99 d~~~A~k~l~~~~~~~~~p~l~~llaA~a-A~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~  175 (398)
T PRK10747         99 DYQQVEKLMTRNADHAEQPVVNYLLAAEA-AQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHG  175 (398)
T ss_pred             CHHHHHHHHHHHHhcccchHHHHHHHHHH-HHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHH
Confidence            788888888876532 1222223332222 23489999999999999875  55654433  336788889999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH-------hhHHHHH
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS-------MLYATAF  182 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-------~t~~~ll  182 (385)
                      +++..+.+                   +.+......+...|.+.|++++|.+++..+.+.+..++.       .+|..++
T Consensus       176 l~~~~~~~-------------------P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~  236 (398)
T PRK10747        176 VDKLLEVA-------------------PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLM  236 (398)
T ss_pred             HHHHHhcC-------------------CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            99987766                   467788999999999999999999999999988754322       1233333


Q ss_pred             HHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCC
Q 040338          183 SARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRN  262 (385)
Q Consensus       183 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~  262 (385)
                      .......+.+...++++.+-+. .                      +.+......+...+...|+.++|..++++..+..
T Consensus       237 ~~~~~~~~~~~l~~~w~~lp~~-~----------------------~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~  293 (398)
T PRK10747        237 DQAMADQGSEGLKRWWKNQSRK-T----------------------RHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQ  293 (398)
T ss_pred             HHHHHhcCHHHHHHHHHhCCHH-H----------------------hCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            3333333333333444433221 1                      2244455677888888899999999998887632


Q ss_pred             hhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHc
Q 040338          263 MISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGL  329 (385)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~  329 (385)
                      ...--.++.+....++.+++++..            .+..+...|.+.+++++|.+.|+...+..+ ...+..+...+.+
T Consensus       294 ~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~  373 (398)
T PRK10747        294 YDERLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDR  373 (398)
T ss_pred             CCHHHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            222223444555668888887777            678889999999999999999999999988 7777889999999


Q ss_pred             cCCHHHHHHHHHhCC
Q 040338          330 SGLLGEAKKLIDEMP  344 (385)
Q Consensus       330 ~g~~~~A~~~~~~m~  344 (385)
                      .|+.++|.+.+++-.
T Consensus       374 ~g~~~~A~~~~~~~l  388 (398)
T PRK10747        374 LHKPEEAAAMRRDGL  388 (398)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            999999999998754

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

Probab=99.44  E-value=2e-13  Score=118.18  Aligned_cols=248  Identities=15%  Similarity=0.094  Sum_probs=85.1

Q ss_pred             cCChHHHHHHHHHHHHhc-cCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           65 VGNIKMALHLHGLVKKFY-FVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      .|++++|+++++...... .+.+...|..+.......++.+.|.+.++++...+                   +.+...+
T Consensus        21 ~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-------------------~~~~~~~   81 (280)
T PF13429_consen   21 RGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-------------------KANPQDY   81 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccc-------------------ccccccc
Confidence            788888888886554443 23355555556666667788888888888887665                   3455667


Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      ..++.. ...+++++|.+++++..+.  .++...+...+..+.+.++++++.++++.+......                
T Consensus        82 ~~l~~l-~~~~~~~~A~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~----------------  142 (280)
T PF13429_consen   82 ERLIQL-LQDGDPEEALKLAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAA----------------  142 (280)
T ss_dssp             ---------------------------------------H-HHHTT-HHHHHHHHHHHHH-T------------------
T ss_pred             cccccc-ccccccccccccccccccc--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCC----------------
Confidence            777776 6788888888888776554  345566667777788888888888888887653221                


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCC
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGP  300 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~  300 (385)
                           +.+...|..+...+.+.|+.++|+..+++..+  | |....+.++..+..                      .|+
T Consensus       143 -----~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~----------------------~~~  195 (280)
T PF13429_consen  143 -----PDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWLLID----------------------MGD  195 (280)
T ss_dssp             ------T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCT----------------------TCH
T ss_pred             -----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH----------------------CCC
Confidence                 12333446666667777788888888888765  4 34455555555544                      445


Q ss_pred             hhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHHHHHHH
Q 040338          301 VTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELVMRNLL  376 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~  376 (385)
                      .+++.++++...+..+  +..+..+..+|...|+.++|...|++... .| |......+..++...|+.++|.++.++..
T Consensus       196 ~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  196 YDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT----------------
T ss_pred             hHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            5555566666555543  56667777888888888888888887765 24 66667777788888888888888777654


Q ss_pred             h
Q 040338          377 Q  377 (385)
Q Consensus       377 ~  377 (385)
                      .
T Consensus       276 ~  276 (280)
T PF13429_consen  276 R  276 (280)
T ss_dssp             -
T ss_pred             c
Confidence            3

>PF13041 PPR_2: PPR repeat family

Probab=99.42  E-value=4e-13  Score=82.68  Aligned_cols=50  Identities=30%  Similarity=0.296  Sum_probs=48.3

Q ss_pred             CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh
Q 040338           47 RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK   99 (385)
Q Consensus        47 ~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~   99 (385)
                      ||+.+||++|.+|++   .|++++|.++|++|.+.|+.||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~---~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCK---AGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHH---CcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            899999999999888   99999999999999999999999999999999985

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

Probab=99.42  E-value=1.1e-10  Score=109.42  Aligned_cols=365  Identities=14%  Similarity=0.077  Sum_probs=226.6

Q ss_pred             CChHHHHHHHHHHHHcccchhh----HHh---------hhhhHHHHHhhhCC--CCh--hhHHHHHHHHHhhhccCChHH
Q 040338            8 KSLPIARKIHAQLISTCLISSI----FLQ---------LIDDDYRVFCDIGP--RYL--FTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         8 ~~~~~a~~~~~~~~~~~~~~~~----~~~---------~~~~A~~~~~~~~~--~~~--~~~~~li~~~~~~~~~~~~~~   70 (385)
                      |+++.+..+.+.+.........    +-+         ++++|...|.+...  +|.  ..+--+-..+..   .|+++.
T Consensus       284 ~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~GlgQm~i~---~~dle~  360 (1018)
T KOG2002|consen  284 KDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGLGQMYIK---RGDLEE  360 (1018)
T ss_pred             ccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccchhHHHHH---hchHHH
Confidence            5666666666666554411111    111         66777766665442  222  222233444444   677777


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcC----ChhHHHHHHHhccCCCccccc------------------cchHHH
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCG----AVDYAESAFLRMLNPSLFCWK------------------FGIIRL  128 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g----~~~~a~~~~~~m~~~~~~~~~------------------~~~~~a  128 (385)
                      +...|+...+.. +.+..+...|...|+..+    ..+.|..++....+..+....                  +-+..|
T Consensus       361 s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~d~~~sL~~~~~A  439 (1018)
T KOG2002|consen  361 SKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQTDPWASLDAYGNA  439 (1018)
T ss_pred             HHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            777777776653 334556666666666554    345555555554443321111                  445555


Q ss_pred             HHHhcC-CCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC---CCCCCH------hhHHHHHHHhcCccCccchhhHH
Q 040338          129 LIMFQK-MPERDLVSWNTMISILTRHGFGFETLCTFIELWNH---GFGLSS------MLYATAFSARASVYDLEWGPHLH  198 (385)
Q Consensus       129 ~~~~~~-~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~p~~------~t~~~ll~~~~~~~~~~~a~~~~  198 (385)
                      ..++.. +..+.+...|.+...+...|.+.+|...|......   -..+|.      .+--.+.+..-..++.+.|.++|
T Consensus       440 ~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Y  519 (1018)
T KOG2002|consen  440 LDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMY  519 (1018)
T ss_pred             HHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHH
Confidence            544433 33456677888888888889999998888887654   122333      23334555666777888888888


Q ss_pred             HHHHHhCCCCchHHHHHHHHHHHhcCCCC-------------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhcc
Q 040338          199 SRVVHMEPSLDVFVGSGLIDMYLKCGCNG-------------------IESSIQIGKALVTMYAEGGSTQKADLAFELMS  259 (385)
Q Consensus       199 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~-------------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  259 (385)
                      ..+.+..+        ..|++|.+.|...                   ...+...++.+...+.+...+..|.+-|+.+.
T Consensus       520 k~Ilkehp--------~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~  591 (1018)
T KOG2002|consen  520 KSILKEHP--------GYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETIL  591 (1018)
T ss_pred             HHHHHHCc--------hhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHH
Confidence            88887643        3455555554111                   45555666667777777777777777665554


Q ss_pred             c-----CChhhHHHHHHHHHhc------------CCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHH
Q 040338          260 R-----RNMISWMVLISAFSQA------------GVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTA  310 (385)
Q Consensus       260 ~-----~~~~~~~~li~~~~~~------------g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~  310 (385)
                      +     +|..+.-+|.+.|.+.            +..++|+++|            +-|-+.-.++..|++..|..||..
T Consensus       592 ~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsq  671 (1018)
T KOG2002|consen  592 KKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQ  671 (1018)
T ss_pred             hhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHH
Confidence            3     2444444444444321            2234555555            233444555677888999999998


Q ss_pred             HHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCCC
Q 040338          311 MAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       311 ~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      ..+...  ..+|--+..+|..+|++..|+++|+....+    .+......|.+++.+.|.+.+|.+.+.......|.++.
T Consensus       672 VrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~  751 (1018)
T KOG2002|consen  672 VREATSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTS  751 (1018)
T ss_pred             HHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccch
Confidence            888766  777778888899999999999998877653    45667778888888889999998888888887777653

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

Probab=99.41  E-value=2.2e-09  Score=91.49  Aligned_cols=294  Identities=12%  Similarity=-0.026  Sum_probs=232.4

Q ss_pred             HHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHh
Q 040338           53 NTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMF  132 (385)
Q Consensus        53 ~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~  132 (385)
                      ..+..++.+ ...|++..|+++..+-.+.+-. ....|-.-..+--..|+.+.+-+.+.+..+.-.              
T Consensus        86 ~~~~egl~~-l~eG~~~qAEkl~~rnae~~e~-p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~--------------  149 (400)
T COG3071          86 KALNEGLLK-LFEGDFQQAEKLLRRNAEHGEQ-PVLAYLLAAEAAQQRGDEDRANRYLAEAAELAG--------------  149 (400)
T ss_pred             HHHHHHHHH-HhcCcHHHHHHHHHHhhhcCcc-hHHHHHHHHHHHHhcccHHHHHHHHHHHhccCC--------------
Confidence            345555444 2379999999999998777644 334455666777788999999999999877633              


Q ss_pred             cCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHH
Q 040338          133 QKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFV  212 (385)
Q Consensus       133 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  212 (385)
                          .++...+-+........|+++.|..-++.+.+.+.. +.........+|.+.|++.....+...+.+.|.-.+...
T Consensus       150 ----~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~  224 (400)
T COG3071         150 ----DDTLAVELTRARLLLNRRDYPAARENVDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEA  224 (400)
T ss_pred             ----CchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHH
Confidence                567777888888999999999999999999886322 566778899999999999999999999999987555433


Q ss_pred             HHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH---
Q 040338          213 GSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF---  286 (385)
Q Consensus       213 ~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~---  286 (385)
                      -               .....+|..+++-....+..+.-...|+..+.   .++..-..++.-+.+.|+.++|.++.   
T Consensus       225 ~---------------~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~  289 (400)
T COG3071         225 A---------------RLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDA  289 (400)
T ss_pred             H---------------HHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            2               23455677788877777778887778888765   36777778888899999999998887   


Q ss_pred             -------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHH
Q 040338          287 -------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALL  356 (385)
Q Consensus       287 -------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li  356 (385)
                             . -...-.+.+.++.+.-++..+.-.+..+  +..+.+|...|.+.+.|.+|...|+..... |+..+|+.+.
T Consensus       290 Lk~~~D~~-L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la  368 (400)
T COG3071         290 LKRQWDPR-LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELA  368 (400)
T ss_pred             HHhccChh-HHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHH
Confidence                   3 2333455677888888888877666555  888999999999999999999999987764 9999999999


Q ss_pred             HHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          357 GACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .++.+.|+..+|.+..++..-.-..|+
T Consensus       369 ~~~~~~g~~~~A~~~r~e~L~~~~~~~  395 (400)
T COG3071         369 DALDQLGEPEEAEQVRREALLLTRQPN  395 (400)
T ss_pred             HHHHHcCChHHHHHHHHHHHHHhcCCC
Confidence            999999999999999999875444443

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

Probab=99.41  E-value=4.4e-13  Score=115.99  Aligned_cols=227  Identities=14%  Similarity=0.074  Sum_probs=93.9

Q ss_pred             hHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCC
Q 040338           92 SSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGF  171 (385)
Q Consensus        92 ~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  171 (385)
                      .+...+.+.|++++|++++++-.....                 ++.|...|..+....-..++++.|...++++...+.
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~-----------------~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~   75 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIA-----------------PPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDK   75 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccc-----------------cccccccccccccccccccccccccccccccccccc
Confidence            557788889999999999955433221                 033455555566667778899999999999987643


Q ss_pred             CCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHH
Q 040338          172 GLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKA  251 (385)
Q Consensus       172 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A  251 (385)
                      . +...+..++.. ...+++++|.++++...+..  ++                      ...+..++..+...++++++
T Consensus        76 ~-~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~~--~~----------------------~~~l~~~l~~~~~~~~~~~~  129 (280)
T PF13429_consen   76 A-NPQDYERLIQL-LQDGDPEEALKLAEKAYERD--GD----------------------PRYLLSALQLYYRLGDYDEA  129 (280)
T ss_dssp             --------------------------------------------------------------------H-HHHTT-HHHH
T ss_pred             c-ccccccccccc-cccccccccccccccccccc--cc----------------------cchhhHHHHHHHHHhHHHHH
Confidence            3 45566667666 68899999998887765543  22                      22345566677778899999


Q ss_pred             HHHHHhccc-----CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHH
Q 040338          252 DLAFELMSR-----RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMV  324 (385)
Q Consensus       252 ~~~~~~m~~-----~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li  324 (385)
                      .++++...+     ++...                      |..+...+.+.|+.++|.+.+++..+..+  ......++
T Consensus       130 ~~~l~~~~~~~~~~~~~~~----------------------~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~  187 (280)
T PF13429_consen  130 EELLEKLEELPAAPDSARF----------------------WLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALA  187 (280)
T ss_dssp             HHHHHHHHH-T---T-HHH----------------------HHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHH
T ss_pred             HHHHHHHHhccCCCCCHHH----------------------HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            999888653     12223                      33344455566778888999999999888  77888999


Q ss_pred             HHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          325 DLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       325 ~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ..+...|+.+++.++++.....  .|...|..+..+|...|+.++|+..+++..+.+|.++
T Consensus       188 ~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~  248 (280)
T PF13429_consen  188 WLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDP  248 (280)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence            9999999999988888777653  5667888999999999999999999999999888654

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

Probab=99.38  E-value=9.4e-10  Score=91.17  Aligned_cols=287  Identities=13%  Similarity=0.050  Sum_probs=200.6

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      +..|-.-++.+..    .+.++|.++|-+|.+.. +.+.++.-+|-+.|.+.|.++.|+++-+.+.+             
T Consensus        36 sr~Yv~GlNfLLs----~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~-------------   97 (389)
T COG2956          36 SRDYVKGLNFLLS----NQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLE-------------   97 (389)
T ss_pred             cHHHHhHHHHHhh----cCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhc-------------
Confidence            3345445544433    88899999999998743 33556667788899999999999998877644             


Q ss_pred             HHHhcCCCCCCc------chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHH
Q 040338          129 LIMFQKMPERDL------VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVV  202 (385)
Q Consensus       129 ~~~~~~~~~~~~------~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  202 (385)
                              .||.      ..--.|..=|...|-+|.|..+|..+.+.|. .-....-.|+..|-...+|++|+++-+++.
T Consensus        98 --------spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~  168 (389)
T COG2956          98 --------SPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLV  168 (389)
T ss_pred             --------CCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                    2332      2233455667888888999999988876532 123445668888888888999998888888


Q ss_pred             HhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCCh---hhHHHHHHHHHhcCCC
Q 040338          203 HMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNM---ISWMVLISAFSQAGVL  279 (385)
Q Consensus       203 ~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~---~~~~~li~~~~~~g~~  279 (385)
                      +.+..+...-.   .               ..|.-+...+....+.+.|..++.+..+.|.   ..--.+.......|++
T Consensus       169 k~~~q~~~~eI---A---------------qfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y  230 (389)
T COG2956         169 KLGGQTYRVEI---A---------------QFYCELAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDY  230 (389)
T ss_pred             HcCCccchhHH---H---------------HHHHHHHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccch
Confidence            87765443211   1               2234455666666788888888887776433   3333455677888888


Q ss_pred             CchHHHH-------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHH-HHhCC
Q 040338          280 EKPRFFF-------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKL-IDEMP  344 (385)
Q Consensus       280 ~~a~~~~-------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~-~~~m~  344 (385)
                      +.|++.|             +...+..+|...|+.++...++..+.+... ......+-+......-.+.|... .+.+.
T Consensus       231 ~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~  310 (389)
T COG2956         231 QKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGADAELMLADLIELQEGIDAAQAYLTRQLR  310 (389)
T ss_pred             HHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHHHh
Confidence            8888888             778888999999999999999999888777 55555555555544445555554 55666


Q ss_pred             CCCCcchHHHHHHHHHhc---CChHHHHHHHHHHHhccc
Q 040338          345 SKPTCVIWGALLGACCSH---YNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       345 ~~p~~~~~~~li~~~~~~---g~~~~a~~~~~~~~~~~~  380 (385)
                      .+|+...+..|+..-...   |...+...+++.|....+
T Consensus       311 r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge~l  349 (389)
T COG2956         311 RKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGEQL  349 (389)
T ss_pred             hCCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHHHH
Confidence            679999999999876543   345677777788775444

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

Probab=99.35  E-value=6.1e-11  Score=106.96  Aligned_cols=274  Identities=14%  Similarity=0.022  Sum_probs=158.1

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcccc-----------ccchHHHHHHh-
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW-----------KFGIIRLLIMF-  132 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~-----------~~~~~~a~~~~-  132 (385)
                      .-+.++|...|...... +.-+..+...+..+|.+.++.++|.++|+.+++......           .-+-+-++.++ 
T Consensus       332 ~y~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~La  410 (638)
T KOG1126|consen  332 QYNCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLA  410 (638)
T ss_pred             HHHHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHH
Confidence            34567777787774333 344456667777888888888888888888766543110           00000011110 


Q ss_pred             ---cCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCC
Q 040338          133 ---QKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL  208 (385)
Q Consensus       133 ---~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  208 (385)
                         -.+.+..+.+|.++.++|.-.++.+.|++.|++...  +.| ...+|+.+-.-+.....+|.|...|+..+    ..
T Consensus       411 q~Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al----~~  484 (638)
T KOG1126|consen  411 QDLIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRKAL----GV  484 (638)
T ss_pred             HHHHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHhhh----cC
Confidence               001123344555555555555555555555555443  233 34444444444444455555555554442    22


Q ss_pred             chHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHH
Q 040338          209 DVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFF  288 (385)
Q Consensus       209 ~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  288 (385)
                      |+..|                   .+|--+...|.+.++++.|+-.|++..+-|...  ..                 ..
T Consensus       485 ~~rhY-------------------nAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~n--sv-----------------i~  526 (638)
T KOG1126|consen  485 DPRHY-------------------NAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSN--SV-----------------IL  526 (638)
T ss_pred             Cchhh-------------------HHHHhhhhheeccchhhHHHHHHHhhhcCCccc--hh-----------------HH
Confidence            23333                   233444555555555555555555544311110  00                 22


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHHHHHhcCC
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLGACCSHYN  364 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~~~~~~g~  364 (385)
                      ..+...+-+.|+.++|.++++++....+  +-.--..+..+...+++++|...++++++- |+ ...|-.+...|.+.|+
T Consensus       527 ~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~  606 (638)
T KOG1126|consen  527 CHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGN  606 (638)
T ss_pred             hhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHcc
Confidence            2333444556777788888888888777  333333566677889999999999999874 54 4567778889999999


Q ss_pred             hHHHHHHHHHHHhccccCC
Q 040338          365 TKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       365 ~~~a~~~~~~~~~~~~~~~  383 (385)
                      .+.|+.=|--+.+++|++.
T Consensus       607 ~~~Al~~f~~A~~ldpkg~  625 (638)
T KOG1126|consen  607 TDLALLHFSWALDLDPKGA  625 (638)
T ss_pred             chHHHHhhHHHhcCCCccc
Confidence            9999999988888888764

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

Probab=99.34  E-value=1.6e-09  Score=101.83  Aligned_cols=81  Identities=14%  Similarity=0.086  Sum_probs=68.4

Q ss_pred             CChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          299 GPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       299 ~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      +..++|.++|.++.+..+  ...-|-+.-.++..|++++|..+|....+.  ....+|-.+.++|...|++..|++.|+.
T Consensus       626 k~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~  705 (1018)
T KOG2002|consen  626 KHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYEN  705 (1018)
T ss_pred             HHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHH
Confidence            456788899999888888  455566888899999999999999999875  3567899999999999999999999998


Q ss_pred             HHhcc
Q 040338          375 LLQLD  379 (385)
Q Consensus       375 ~~~~~  379 (385)
                      ..+.-
T Consensus       706 ~lkkf  710 (1018)
T KOG2002|consen  706 CLKKF  710 (1018)
T ss_pred             HHHHh
Confidence            76543

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

Probab=99.32  E-value=2.9e-09  Score=99.42  Aligned_cols=339  Identities=10%  Similarity=0.057  Sum_probs=214.2

Q ss_pred             hhhhHHHHHhhhCC---CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIGP---RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|.+++.++.+   .+...|-+|-..|-.   .|+.+++...+-...... +.|...|..+-....+.|+++.|.-.
T Consensus       154 ~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEq---rGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~i~qA~~c  229 (895)
T KOG2076|consen  154 DLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQ---RGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGNINQARYC  229 (895)
T ss_pred             CHHHHHHHHHHHHHhCccchhhHHHHHHHHHH---cccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhcccHHHHHHH
Confidence            89999999988873   456688888888777   899999998875554433 44668899999999999999999999


Q ss_pred             HHhccCCCccccc------------cchHHHHHHhcCCCC----CCcchHHH----HHHHHHhCCCchHHHHHHHHHHHC
Q 040338          110 FLRMLNPSLFCWK------------FGIIRLLIMFQKMPE----RDLVSWNT----MISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       110 ~~~m~~~~~~~~~------------~~~~~a~~~~~~~~~----~~~~~~~~----li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      |.+..+.++..|.            |+...|..-|.++-+    .|..-+..    .+..+...++-+.|.+.++.....
T Consensus       230 y~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~  309 (895)
T KOG2076|consen  230 YSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGALSK  309 (895)
T ss_pred             HHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhh
Confidence            9999887764444            555555554444322    12122222    233444455556666655555442


Q ss_pred             C-CCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH------HHHHHhcCCCCCCchhhHHHHHHHHH
Q 040338          170 G-FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL------IDMYLKCGCNGIESSIQIGKALVTMY  242 (385)
Q Consensus       170 g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l------i~~~~~~g~~~~~~~~~~~~~li~~~  242 (385)
                      + -..+...+++++..+.+..+++.+......+.....++|..-+.+-      ...++..| .+..++..++ .+.-++
T Consensus       310 ~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~-~~~s~~l~v~-rl~icL  387 (895)
T KOG2076|consen  310 EKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVG-KELSYDLRVI-RLMICL  387 (895)
T ss_pred             ccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCC-CCCCccchhH-hHhhhh
Confidence            2 2234445555566666666666666665555553333333332100      00011111 0033333331 222233


Q ss_pred             HcCCChhHHHHHHHhccc------CChhhHHHHHHHHHhcCCCCchHHHH-------------HHHHHHHHhcccCChhh
Q 040338          243 AEGGSTQKADLAFELMSR------RNMISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTK  303 (385)
Q Consensus       243 ~~~g~~~~A~~~~~~m~~------~~~~~~~~li~~~~~~g~~~~a~~~~-------------~~~~l~~~~~~~~~~~~  303 (385)
                      ......+....+.....+      .+...|.-+..+|.+.|++.+|+.++             .|-.+..+|...|..+.
T Consensus       388 ~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~  467 (895)
T KOG2076|consen  388 VHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEE  467 (895)
T ss_pred             hcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHH
Confidence            333333333333333333      24567888889999999999999998             77888888899999999


Q ss_pred             HHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-----------CCcchHHHHHHHHHhcCChHHHHH
Q 040338          304 GKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-----------PTCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       304 a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----------p~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      |.+.|+......+  ...-..|-..+-+.|+.++|.+.++.+...           |+...--.....+...|+.++-..
T Consensus       468 A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~E~fi~  547 (895)
T KOG2076|consen  468 AIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKREEFIN  547 (895)
T ss_pred             HHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhHHHHHH
Confidence            9999999888777  666677788888999999999999886531           333333345556777888877666


Q ss_pred             HHHHHHh
Q 040338          371 VMRNLLQ  377 (385)
Q Consensus       371 ~~~~~~~  377 (385)
                      ..-+|+.
T Consensus       548 t~~~Lv~  554 (895)
T KOG2076|consen  548 TASTLVD  554 (895)
T ss_pred             HHHHHHH
Confidence            6665554

>TIGR00540 hemY_coli hemY protein

Probab=99.30  E-value=1.8e-09  Score=98.48  Aligned_cols=271  Identities=10%  Similarity=-0.050  Sum_probs=182.8

Q ss_pred             hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHH
Q 040338           33 LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF  110 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~  110 (385)
                      +++.|.+.+.+..  .|++.. +.++.+-. ....|+.+.|.+.+....+....+....--.....+...|+.+.|...+
T Consensus        99 ~~~~A~~~l~~~~~~~~~~~~-~~llaA~a-a~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l  176 (409)
T TIGR00540        99 DYAKAEKLIAKNADHAAEPVL-NLIKAAEA-AQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHGV  176 (409)
T ss_pred             CHHHHHHHHHHHhhcCCCCHH-HHHHHHHH-HHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHH
Confidence            8888888887766  344332 33333322 2237999999999999987532222234444578888899999999999


Q ss_pred             HhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHH---hcC
Q 040338          111 LRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSA---RAS  187 (385)
Q Consensus       111 ~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~---~~~  187 (385)
                      +.+.+..                   +.+..+...+...+.+.|++++|.+.+..+.+.++.+.......-..+   ...
T Consensus       177 ~~l~~~~-------------------P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~  237 (409)
T TIGR00540       177 DKLLEMA-------------------PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLD  237 (409)
T ss_pred             HHHHHhC-------------------CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            9998776                   356778889999999999999999999999998754332221111111   123


Q ss_pred             ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhh
Q 040338          188 VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMIS  265 (385)
Q Consensus       188 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~  265 (385)
                      .+..+.+.+.+..+.+..+..                   .+.+...+..+...+...|+.++|.+++++..+  ||...
T Consensus       238 ~~~~~~~~~~L~~~~~~~p~~-------------------~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~  298 (409)
T TIGR00540       238 EAMADEGIDGLLNWWKNQPRH-------------------RRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRA  298 (409)
T ss_pred             HHHHhcCHHHHHHHHHHCCHH-------------------HhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCccc
Confidence            333444445555555443210                   012445556777788888899999999988876  44331


Q ss_pred             H-HHHHHHH--HhcCCCCchHHHH--------------HHHHHHHHhcccCChhhHHHHHH--HHHhccc-hhhHHHHHH
Q 040338          266 W-MVLISAF--SQAGVLEKPRFFF--------------FFVSLLSGCSHSGPVTKGKHYFT--AMAKFTY-TCYFVCMVD  325 (385)
Q Consensus       266 ~-~~li~~~--~~~g~~~~a~~~~--------------~~~~l~~~~~~~~~~~~a~~~~~--~~~~~~~-~~~~~~li~  325 (385)
                      . ..++..+  ...++.+.+++.+              ...++...|.+.|++++|.+.|+  ...+..+ ...+..+..
T Consensus       299 ~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~  378 (409)
T TIGR00540       299 ISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAAD  378 (409)
T ss_pred             chhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHH
Confidence            1 0122322  2334444454444              24467788889999999999999  4555555 666779999


Q ss_pred             HHHccCCHHHHHHHHHhC
Q 040338          326 LLGLSGLLGEAKKLIDEM  343 (385)
Q Consensus       326 ~~~~~g~~~~A~~~~~~m  343 (385)
                      .+.+.|+.++|.+++++.
T Consensus       379 ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       379 AFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHcCCHHHHHHHHHHH
Confidence            999999999999999875

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.

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

Probab=99.29  E-value=1.5e-08  Score=88.28  Aligned_cols=345  Identities=12%  Similarity=0.037  Sum_probs=211.4

Q ss_pred             CCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHh-hhC-CCChhhHHHHHHHHHhhhccCChHHHHHH
Q 040338            7 LKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFC-DIG-PRYLFTYNTMINGGVRCLCVGNIKMALHL   74 (385)
Q Consensus         7 ~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~-~~~-~~~~~~~~~li~~~~~~~~~~~~~~a~~~   74 (385)
                      .+.+..|+.|+++++.....-+.+-+          ++.-|+++|+ +|. +|+...|++.|.-=.+   -+.++.|..+
T Consensus       120 nk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElR---ykeieraR~I  196 (677)
T KOG1915|consen  120 NKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFERWMEWEPDEQAWLSFIKFELR---YKEIERARSI  196 (677)
T ss_pred             hhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHH---hhHHHHHHHH
Confidence            34566677777777776555555444          7777888886 454 7888888888887555   6778888888


Q ss_pred             HHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCC---c------cccc-----------------------
Q 040338           75 HGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPS---L------FCWK-----------------------  122 (385)
Q Consensus        75 ~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~---~------~~~~-----------------------  122 (385)
                      ++..+-  +.|++..|-.....=-++|++..|.++|+...+.-   .      +.+.                       
T Consensus       197 YerfV~--~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~  274 (677)
T KOG1915|consen  197 YERFVL--VHPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHI  274 (677)
T ss_pred             HHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            887775  35777777777777777777777777776653210   0      0000                       


Q ss_pred             -------------------cchHHHHHHh--------cCCC---CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCC
Q 040338          123 -------------------FGIIRLLIMF--------QKMP---ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFG  172 (385)
Q Consensus       123 -------------------~~~~~a~~~~--------~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  172 (385)
                                         |+.....+..        ..+.   +.|-.+|--.+..-...|+.+...++|++.... ++
T Consensus       275 pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vp  353 (677)
T KOG1915|consen  275 PKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VP  353 (677)
T ss_pred             CcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CC
Confidence                               2211111111        0011   123334444555555667777777777777654 44


Q ss_pred             CCHh-----hHHH-HHH-Hh---cCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHH
Q 040338          173 LSSM-----LYAT-AFS-AR---ASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMY  242 (385)
Q Consensus       173 p~~~-----t~~~-ll~-~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~  242 (385)
                      |-..     -|-. .|+ +|   ....|.+.+.++++..++. ++....||..+=-+|+                  ..-
T Consensus       354 p~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l-IPHkkFtFaKiWlmyA------------------~fe  414 (677)
T KOG1915|consen  354 PASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL-IPHKKFTFAKIWLMYA------------------QFE  414 (677)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-cCcccchHHHHHHHHH------------------HHH
Confidence            4211     0111 111 11   2445666666777766663 3444455544333332                  222


Q ss_pred             HcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHH
Q 040338          243 AEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       243 ~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      .++.++..|.+++.....  |...+|..-|..=.+.+++++...++            +|......-...|+.+.|..+|
T Consensus       415 IRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaif  494 (677)
T KOG1915|consen  415 IRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIF  494 (677)
T ss_pred             HHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHH
Confidence            345677777777765543  66666666676666777777777776            6666666666778888888888


Q ss_pred             HHHHhccc----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHH-----hcC-----------ChHH
Q 040338          309 TAMAKFTY----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACC-----SHY-----------NTKL  367 (385)
Q Consensus       309 ~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~-----~~g-----------~~~~  367 (385)
                      +-....+.    ...+.+.|+.-...|.++.|..++++..+. +...+|-.+...-.     ..+           ....
T Consensus       495 elAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~h~kvWisFA~fe~s~~~~~~~~~~~~~e~~~~~~~~  574 (677)
T KOG1915|consen  495 ELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQHVKVWISFAKFEASASEGQEDEDLAELEITDENIKR  574 (677)
T ss_pred             HHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhcccchHHHhHHHHhccccccccccchhhhhcchhHHHH
Confidence            88888776    556667777777888888899888888775 56667777665544     223           3456


Q ss_pred             HHHHHHHHH
Q 040338          368 AELVMRNLL  376 (385)
Q Consensus       368 a~~~~~~~~  376 (385)
                      |..+|++..
T Consensus       575 AR~iferAn  583 (677)
T KOG1915|consen  575 ARKIFERAN  583 (677)
T ss_pred             HHHHHHHHH
Confidence            677776653

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

Probab=99.26  E-value=1.7e-08  Score=83.87  Aligned_cols=279  Identities=15%  Similarity=0.075  Sum_probs=195.1

Q ss_pred             cchhhHHh-------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC---chHHHhHH
Q 040338           25 LISSIFLQ-------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD---ESIAKSSI   94 (385)
Q Consensus        25 ~~~~~~~~-------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~li   94 (385)
                      +..+.+..       ..++|.++|-+|.+-|+.||.+=+.--.-+.++|.+++|+++++.+.++.--+.   ....-.|.
T Consensus        35 lsr~Yv~GlNfLLs~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~  114 (389)
T COG2956          35 LSRDYVKGLNFLLSNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLG  114 (389)
T ss_pred             ccHHHHhHHHHHhhcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHH
Confidence            44555554       899999999999987877776433322223349999999999999998521111   12334566


Q ss_pred             HHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC
Q 040338           95 DMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS  174 (385)
Q Consensus        95 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  174 (385)
                      .=|...|-++.|+.+|..+.+.+                   ..-...-.-|+..|-...+|++|+++-+++.+.|-.+.
T Consensus       115 ~Dym~aGl~DRAE~~f~~L~de~-------------------efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~  175 (389)
T COG2956         115 RDYMAAGLLDRAEDIFNQLVDEG-------------------EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTY  175 (389)
T ss_pred             HHHHHhhhhhHHHHHHHHHhcch-------------------hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccc
Confidence            77788899999999998887644                   23445677799999999999999999999988765553


Q ss_pred             ----HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhH
Q 040338          175 ----SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQK  250 (385)
Q Consensus       175 ----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~  250 (385)
                          ...|.-+...+....+++.|...+....+.+.+...                       .--.+.+.....|+++.
T Consensus       176 ~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvR-----------------------Asi~lG~v~~~~g~y~~  232 (389)
T COG2956         176 RVEIAQFYCELAQQALASSDVDRARELLKKALQADKKCVR-----------------------ASIILGRVELAKGDYQK  232 (389)
T ss_pred             hhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCcccee-----------------------hhhhhhHHHHhccchHH
Confidence                234566777777778899999999998887653222                       22345677788899999


Q ss_pred             HHHHHHhcccCCh----hhHHHHHHHHHhcCCCCchHHHH-----------HHHHHHHHhcccCChhhHHHHHHHHHhcc
Q 040338          251 ADLAFELMSRRNM----ISWMVLISAFSQAGVLEKPRFFF-----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFT  315 (385)
Q Consensus       251 A~~~~~~m~~~~~----~~~~~li~~~~~~g~~~~a~~~~-----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  315 (385)
                      |.+.++...+.|.    .+...|..+|.+.|++++....+           .-..+-..-....-.+.|...+.+-.+..
T Consensus       233 AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~  312 (389)
T COG2956         233 AVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGADAELMLADLIELQEGIDAAQAYLTRQLRRK  312 (389)
T ss_pred             HHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHHHhhC
Confidence            9999999988655    45667889999999999988877           22222222222333455555555544444


Q ss_pred             c-hhhHHHHHHHHHc---cCCHHHHHHHHHhCCC
Q 040338          316 Y-TCYFVCMVDLLGL---SGLLGEAKKLIDEMPS  345 (385)
Q Consensus       316 ~-~~~~~~li~~~~~---~g~~~~A~~~~~~m~~  345 (385)
                      + ...+..+|+.-..   -|+..+-..+++.|..
T Consensus       313 Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvg  346 (389)
T COG2956         313 PTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVG  346 (389)
T ss_pred             CcHHHHHHHHHhhhccccccchhhhHHHHHHHHH
Confidence            4 7777778877654   4456666666666643

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

Probab=99.22  E-value=9.4e-09  Score=89.30  Aligned_cols=294  Identities=13%  Similarity=0.037  Sum_probs=219.8

Q ss_pred             CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccc---------cchHHHHHHhcCCCCCCcchHH-HHHHHHHhC
Q 040338           84 VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK---------FGIIRLLIMFQKMPERDLVSWN-TMISILTRH  153 (385)
Q Consensus        84 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~-~li~~~~~~  153 (385)
                      .-|...+-.....+-+.|..+.|.+.|......-+.-|.         .+++.+..+-...+..+...-. -+..++...
T Consensus       161 ~~D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~~P~~W~AWleL~~lit~~e~~~~l~~~l~~~~h~M~~~F~~~a~~el  240 (559)
T KOG1155|consen  161 EKDEFLLYLYGVVLKELGLLSLAIDSFVEVVNRYPWFWSAWLELSELITDIEILSILVVGLPSDMHWMKKFFLKKAYQEL  240 (559)
T ss_pred             cchhHHHHHHHHHHHhhchHHHHHHHHHHHHhcCCcchHHHHHHHHhhchHHHHHHHHhcCcccchHHHHHHHHHHHHHH
Confidence            334444444445556678888899888887765555554         3333333333333221111111 233566666


Q ss_pred             CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC--CCchHHHHHHHHHHHhcCCCC----
Q 040338          154 GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP--SLDVFVGSGLIDMYLKCGCNG----  227 (385)
Q Consensus       154 ~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~li~~~~~~g~~~----  227 (385)
                      .+.+++..=.+.....|++-+...-+....+.-...|+++|+.+|+++.+..+  --|..+|+.++-.--......    
T Consensus       241 ~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~  320 (559)
T KOG1155|consen  241 HQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQ  320 (559)
T ss_pred             HHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHH
Confidence            78888888888888888776665555566666788999999999999999854  236677776654433222111    


Q ss_pred             -----CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH------------H
Q 040338          228 -----IESSIQIGKALVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF------------F  287 (385)
Q Consensus       228 -----~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~------------~  287 (385)
                           .+--..|...+.+-|.-.++.++|...|+...+-   -...|+.+.+-|....+...|++-+            .
T Consensus       321 ~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRA  400 (559)
T KOG1155|consen  321 NVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRA  400 (559)
T ss_pred             HHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHH
Confidence                 3334456777888888889999999999988763   4578888999999999999999888            8


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g  363 (385)
                      |-.+.++|.-.+...-|.-.|++.....+  +..+.+|.++|.+.++.++|++-|.+...-  .+...+..|.+.|-+.+
T Consensus       401 WYGLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~  480 (559)
T KOG1155|consen  401 WYGLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELK  480 (559)
T ss_pred             HhhhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHH
Confidence            99999999999999999999999998888  999999999999999999999999988764  44578999999999999


Q ss_pred             ChHHHHHHHHHHHh
Q 040338          364 NTKLAELVMRNLLQ  377 (385)
Q Consensus       364 ~~~~a~~~~~~~~~  377 (385)
                      +.++|-..+++.++
T Consensus       481 d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  481 DLNEAAQYYEKYVE  494 (559)
T ss_pred             hHHHHHHHHHHHHH
Confidence            99999999998776

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

Probab=99.21  E-value=3.8e-08  Score=84.46  Aligned_cols=286  Identities=11%  Similarity=0.008  Sum_probs=202.7

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHHHHHh-ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHh
Q 040338           54 TMINGGVRCLCVGNIKMALHLHGLVKKF-YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMF  132 (385)
Q Consensus        54 ~li~~~~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~  132 (385)
                      .=|.+++.|. .++-..+...+-.+... -++-|+.....+.+++...|+.++|+..|++....++              
T Consensus       199 ~wika~Aq~~-~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dp--------------  263 (564)
T KOG1174|consen  199 KWIKALAQMF-NFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANP--------------  263 (564)
T ss_pred             HHHHHHHHHH-hcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCCh--------------
Confidence            3455555433 34444444444333332 3667888899999999999999999999988765542              


Q ss_pred             cCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHH
Q 040338          133 QKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFV  212 (385)
Q Consensus       133 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  212 (385)
                           -++.........+.+.|+++....+...+... .+-+...|..-.......++++.|+.+-+..++....     
T Consensus       264 -----y~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~-~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r-----  332 (564)
T KOG1174|consen  264 -----DNVEAMDLYAVLLGQEGGCEQDSALMDYLFAK-VKYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPR-----  332 (564)
T ss_pred             -----hhhhhHHHHHHHHHhccCHhhHHHHHHHHHhh-hhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcc-----
Confidence                 22222233333456788888888888777653 1123333333333445667888888888877765431     


Q ss_pred             HHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH--H
Q 040338          213 GSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF--F  287 (385)
Q Consensus       213 ~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~--~  287 (385)
                                        ++..+-.-.+.+...|+.++|.--|+..+.  | +..+|..|+..|...|++.+|.-+-  +
T Consensus       333 ------------------~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~  394 (564)
T KOG1174|consen  333 ------------------NHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWT  394 (564)
T ss_pred             ------------------cchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHH
Confidence                              222223334556677899999999987654  4 7899999999999999999987655  2


Q ss_pred             H----------HHHH-HHhc-ccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchH
Q 040338          288 F----------VSLL-SGCS-HSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIW  352 (385)
Q Consensus       288 ~----------~~l~-~~~~-~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~  352 (385)
                      +          +.+. ..|. ....-++|..++++..+..+  ....+.+.+.+...|+.++++.+++..... ||....
T Consensus       395 ~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH  474 (564)
T KOG1174|consen  395 IRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLH  474 (564)
T ss_pred             HHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHH
Confidence            2          2221 1121 23456889999999888877  777888889999999999999999988775 999999


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          353 GALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       353 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +.|.+.+...+.+++|+.-|...++.+|++-
T Consensus       475 ~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~~  505 (564)
T KOG1174|consen  475 NHLGDIMRAQNEPQKAMEYYYKALRQDPKSK  505 (564)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhcCccch
Confidence            9999999999999999999999999998763

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

Probab=99.20  E-value=2.5e-08  Score=93.33  Aligned_cols=289  Identities=12%  Similarity=0.093  Sum_probs=185.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|.+++.+.++.. +.+...|.+|...|-..|+.+++...+--....+                   +.|..-|.
T Consensus       152 rg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-------------------p~d~e~W~  211 (895)
T KOG2076|consen  152 RGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-------------------PKDYELWK  211 (895)
T ss_pred             hCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-------------------CCChHHHH
Confidence            599999999999999975 5588899999999999999999998875554333                   23444555


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchH-------------
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVF-------------  211 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------------  211 (385)
                      .+-....+.|.++.|.-+|.+..+. -+++...+--=...|-+.|+...|..-|.++.+..++.|..             
T Consensus       212 ~ladls~~~~~i~qA~~cy~rAI~~-~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~  290 (895)
T KOG2076|consen  212 RLADLSEQLGNINQARYCYSRAIQA-NPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYF  290 (895)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHhc-CCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHH
Confidence            5555555555555555555555543 12233333333444555555555555555555443322211             


Q ss_pred             --------HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----C------------------
Q 040338          212 --------VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR----R------------------  261 (385)
Q Consensus       212 --------~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~------------------  261 (385)
                              ....|-.++.+.+   ..-+...++.++..+.+...++.|......+..    +                  
T Consensus       291 ~~~~~~e~a~~~le~~~s~~~---~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~  367 (895)
T KOG2076|consen  291 ITHNERERAAKALEGALSKEK---DEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNAL  367 (895)
T ss_pred             HHhhHHHHHHHHHHHHHhhcc---ccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhcccccccc
Confidence                    1112222222222   123334556777777777788888777766543    1                  


Q ss_pred             ----ChhhHHH----HHHHHH--hcCCCCchHHHH-------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--
Q 040338          262 ----NMISWMV----LISAFS--QAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--  316 (385)
Q Consensus       262 ----~~~~~~~----li~~~~--~~g~~~~a~~~~-------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--  316 (385)
                          +..+|..    ++-++.  +.+...+++.-+             .|..+..++...|++.+|..++..+.....  
T Consensus       368 ~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~  447 (895)
T KOG2076|consen  368 CEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQ  447 (895)
T ss_pred             ccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCcccc
Confidence                1111111    111222  233333443333             788889999999999999999999988777  


Q ss_pred             -hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          317 -TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       317 -~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                       ..+|--+..+|...|.+++|.+.|+..... | +...-.+|...+...|+.++|.+.+..+..
T Consensus       448 ~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~  511 (895)
T KOG2076|consen  448 NAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIIN  511 (895)
T ss_pred             chhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccC
Confidence             668888999999999999999999888764 4 344555677778889999999999888763

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

Probab=99.20  E-value=3e-09  Score=92.12  Aligned_cols=48  Identities=15%  Similarity=0.132  Sum_probs=27.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhcc
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRML  114 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  114 (385)
                      .|.++.|+.-|+...+.  .|+..+--.|+-++.--|+-++..+.|.+|.
T Consensus       289 ~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli  336 (840)
T KOG2003|consen  289 AGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLI  336 (840)
T ss_pred             cccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHh
Confidence            67777777777766654  3554443333333334566666666666663

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

Probab=99.20  E-value=2.8e-10  Score=102.78  Aligned_cols=230  Identities=12%  Similarity=-0.055  Sum_probs=185.0

Q ss_pred             CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC--CCchHHHHHHHHHHHhcCCCC----
Q 040338          154 GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP--SLDVFVGSGLIDMYLKCGCNG----  227 (385)
Q Consensus       154 ~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~li~~~~~~g~~~----  227 (385)
                      -+..+|+..|.+...+ +.-+......+-++|...+++++++++|+.+.+..+  .-+..+|++.+=.+-+.-...    
T Consensus       333 y~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq  411 (638)
T KOG1126|consen  333 YNCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQ  411 (638)
T ss_pred             HHHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHH
Confidence            3577899999885544 333445666788899999999999999999988754  245667777654332222111    


Q ss_pred             -----CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH------------H
Q 040338          228 -----IESSIQIGKALVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF------------F  287 (385)
Q Consensus       228 -----~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~------------~  287 (385)
                           .+....+|.++.++|.-+++.+.|++.|++..+-   ...+|+.+..-+.....+|.|...|            +
T Consensus       412 ~Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnA  491 (638)
T KOG1126|consen  412 DLIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNA  491 (638)
T ss_pred             HHHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHH
Confidence                 4556789999999999999999999999998873   5688888888899999999999999            7


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g  363 (385)
                      |--+.-.|.+.++.+.|+-.|+++.+.++  ......+...+-+.|+.++|+.++++...-  .|+.+----+..+...+
T Consensus       492 wYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~  571 (638)
T KOG1126|consen  492 WYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLG  571 (638)
T ss_pred             HHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhc
Confidence            77888999999999999999999999999  777777888999999999999999988652  34444444556677789


Q ss_pred             ChHHHHHHHHHHHhccccCCC
Q 040338          364 NTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      ++++|+..++++++.-|+.++
T Consensus       572 ~~~eal~~LEeLk~~vP~es~  592 (638)
T KOG1126|consen  572 RYVEALQELEELKELVPQESS  592 (638)
T ss_pred             chHHHHHHHHHHHHhCcchHH
Confidence            999999999999998887653

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.20  E-value=5.4e-09  Score=95.11  Aligned_cols=218  Identities=11%  Similarity=0.057  Sum_probs=171.1

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHC-----C-CCCCHhhH-HHHHHHhcCccCccchhhHHHHHHHhC---CCCch
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNH-----G-FGLSSMLY-ATAFSARASVYDLEWGPHLHSRVVHME---PSLDV  210 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----g-~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~~~  210 (385)
                      .+...|...|...|+++.|+.++....+.     | ..|...+. +.+...|...+++++|..+|+.++..-   +-++.
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            45556889999999999999999887654     3 23444443 346778889999999999999988641   11111


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----------CCh-hhHHHHHHHHHhcCCC
Q 040338          211 FVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR----------RNM-ISWMVLISAFSQAGVL  279 (385)
Q Consensus       211 ~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----------~~~-~~~~~li~~~~~~g~~  279 (385)
                                        +.-..+++.|-..|.+.|++++|...++...+          +.+ .-++.++..++..+++
T Consensus       280 ------------------~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~  341 (508)
T KOG1840|consen  280 ------------------PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEY  341 (508)
T ss_pred             ------------------HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcch
Confidence                              11234567788889999999998888876653          222 3456678889999999


Q ss_pred             CchHHHH--------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc----------hhhHHHHHHHHHc
Q 040338          280 EKPRFFF--------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----------TCYFVCMVDLLGL  329 (385)
Q Consensus       280 ~~a~~~~--------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----------~~~~~~li~~~~~  329 (385)
                      ++|..++                    +++.+...|...|++++|..+++++.....          ...++.+...|.+
T Consensus       342 Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~  421 (508)
T KOG1840|consen  342 EEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEE  421 (508)
T ss_pred             hHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHH
Confidence            9999888                    899999999999999999999999887542          5667788999999


Q ss_pred             cCCHHHHHHHHHhCCC--------CCCc-chHHHHHHHHHhcCChHHHHHHHHHHH
Q 040338          330 SGLLGEAKKLIDEMPS--------KPTC-VIWGALLGACCSHYNTKLAELVMRNLL  376 (385)
Q Consensus       330 ~g~~~~A~~~~~~m~~--------~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~  376 (385)
                      .+++.+|.++|.+...        .|++ .+|..|...|.+.|++++|.++.+...
T Consensus       422 ~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  422 LKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             hcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            9999999999987654        1443 479999999999999999999998876

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

Probab=99.20  E-value=5e-09  Score=90.98  Aligned_cols=124  Identities=8%  Similarity=0.008  Sum_probs=61.9

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      .....|+.+..-|....+...|+.-|+...+. .+.|-..|--|-.+|.-.+...-|+-.|++.....            
T Consensus       362 ~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi-~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k------------  428 (559)
T KOG1155|consen  362 KYLSAWTLMGHEYVEMKNTHAAIESYRRAVDI-NPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK------------  428 (559)
T ss_pred             chhHHHHHhhHHHHHhcccHHHHHHHHHHHhc-CchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC------------
Confidence            33445555555555555555555555555442 12244445555555555555555555555544432            


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-CC--hhhHHHHHHHHHhcCCCCchHHH
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-RN--MISWMVLISAFSQAGVLEKPRFF  285 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~~--~~~~~~li~~~~~~g~~~~a~~~  285 (385)
                                 +.|...|.+|.++|.+.+++++|+..|..... .|  ...+..|...|-+.++.++|...
T Consensus       429 -----------PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~  488 (559)
T KOG1155|consen  429 -----------PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQY  488 (559)
T ss_pred             -----------CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHH
Confidence                       23445555566666666666666666655543 12  24444444444444444444333

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

Probab=99.17  E-value=2.3e-07  Score=81.19  Aligned_cols=347  Identities=12%  Similarity=0.095  Sum_probs=220.9

Q ss_pred             CCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhC----CCChhhHHHHHHHHHhhhccCChHHH
Q 040338            7 LKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIG----PRYLFTYNTMINGGVRCLCVGNIKMA   71 (385)
Q Consensus         7 ~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~~~~a   71 (385)
                      .+++..|++||++++.-. ..++.++           .+..|+.+|++..    +.|-. |-..+-.   --..|++..|
T Consensus        86 q~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdql-WyKY~ym---EE~LgNi~ga  160 (677)
T KOG1915|consen   86 QKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQL-WYKYIYM---EEMLGNIAGA  160 (677)
T ss_pred             HHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHH-HHHHHHH---HHHhcccHHH
Confidence            456788999999998765 3333333           8888999998654    33333 3333322   1227999999


Q ss_pred             HHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHH
Q 040338           72 LHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILT  151 (385)
Q Consensus        72 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~  151 (385)
                      .++|+.-.+  ..|+...|.+.|+.=.+...++.|..+|++..-                    .+|++.+|--....=.
T Consensus       161 RqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~--------------------~HP~v~~wikyarFE~  218 (677)
T KOG1915|consen  161 RQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVL--------------------VHPKVSNWIKYARFEE  218 (677)
T ss_pred             HHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--------------------ecccHHHHHHHHHHHH
Confidence            999998876  689999999999999999999999999987532                    1477777766666666


Q ss_pred             hCCCchHHHHHHHHHHHC-CC-CCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCCC-
Q 040338          152 RHGFGFETLCTFIELWNH-GF-GLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLD-VFVGSGLIDMYLKCGCNG-  227 (385)
Q Consensus       152 ~~~~~~~a~~~~~~m~~~-g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~-  227 (385)
                      ++|+...|..+|+...+. |- .-+...|.+....=.+.+.++.|.-+|...++.-++.. ...|..+..-=-+-|+.. 
T Consensus       219 k~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~g  298 (677)
T KOG1915|consen  219 KHGNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEG  298 (677)
T ss_pred             hcCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhh
Confidence            777777777777766553 10 11222333333333345566666666666665533221 234444443333334333 


Q ss_pred             -------------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-------------------------
Q 040338          228 -------------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-------------------------  261 (385)
Q Consensus       228 -------------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-------------------------  261 (385)
                                         .+.|-.+|--.++.--..|+.+...++|+....  |                         
T Consensus       299 IEd~Iv~KRk~qYE~~v~~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWinYalyeEle  378 (677)
T KOG1915|consen  299 IEDAIVGKRKFQYEKEVSKNPYNYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWINYALYEELE  378 (677)
T ss_pred             hHHHHhhhhhhHHHHHHHhCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence                               333444555555555666666666666665542  1                         


Q ss_pred             --------------------ChhhHHHH----HHHHHhcCCCCchHHHH-----------HHHHHHHHhcccCChhhHHH
Q 040338          262 --------------------NMISWMVL----ISAFSQAGVLEKPRFFF-----------FFVSLLSGCSHSGPVTKGKH  306 (385)
Q Consensus       262 --------------------~~~~~~~l----i~~~~~~g~~~~a~~~~-----------~~~~l~~~~~~~~~~~~a~~  306 (385)
                                          .-.||.-+    ..--.++.++..|.+++           +|-..|+.-.+.++++.+..
T Consensus       379 ~ed~ertr~vyq~~l~lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRk  458 (677)
T KOG1915|consen  379 AEDVERTRQVYQACLDLIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRK  458 (677)
T ss_pred             hhhHHHHHHHHHHHHhhcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHH
Confidence                                11122211    11123445555555555           56666666667788888888


Q ss_pred             HHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCc----chHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          307 YFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTC----VIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       307 ~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      ++++....++  ..++......-...|+.+.|..+|+-....|..    ..|.+.|..-...|.+++|..+++.+++...
T Consensus       459 LYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~  538 (677)
T KOG1915|consen  459 LYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQ  538 (677)
T ss_pred             HHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhcc
Confidence            8888888777  666677777777788888888888887776533    3566666666778888888888888876543

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

Probab=99.15  E-value=5.9e-08  Score=84.31  Aligned_cols=244  Identities=11%  Similarity=0.003  Sum_probs=167.0

Q ss_pred             HHHHhcCChhHHHHHHHhccCCCccccc---------------cchHHHHHHhcCCCCCCcchHHHHH-----HHHHhCC
Q 040338           95 DMHVKCGAVDYAESAFLRMLNPSLFCWK---------------FGIIRLLIMFQKMPERDLVSWNTMI-----SILTRHG  154 (385)
Q Consensus        95 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~---------------~~~~~a~~~~~~~~~~~~~~~~~li-----~~~~~~~  154 (385)
                      .-|.+.|+++.|.++++-..+.+..+..               .++..|..+-+.-  .+..-||.-.     +...-+|
T Consensus       427 ~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~a--ln~dryn~~a~~nkgn~~f~ng  504 (840)
T KOG2003|consen  427 GELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIA--LNIDRYNAAALTNKGNIAFANG  504 (840)
T ss_pred             HHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHH--hcccccCHHHhhcCCceeeecC
Confidence            3567899999999999888776543222               1222222222211  1222233221     1223468


Q ss_pred             CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhH
Q 040338          155 FGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQI  234 (385)
Q Consensus       155 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~  234 (385)
                      ++++|.+.|++.....-.-....|++=+ .+-..|++++|++.|-.+...-                       ..+..+
T Consensus       505 d~dka~~~ykeal~ndasc~ealfnigl-t~e~~~~ldeald~f~klh~il-----------------------~nn~ev  560 (840)
T KOG2003|consen  505 DLDKAAEFYKEALNNDASCTEALFNIGL-TAEALGNLDEALDCFLKLHAIL-----------------------LNNAEV  560 (840)
T ss_pred             cHHHHHHHHHHHHcCchHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHHH-----------------------HhhHHH
Confidence            8888888888887654333344444333 3456678888888776654321                       123344


Q ss_pred             HHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccC
Q 040338          235 GKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSG  299 (385)
Q Consensus       235 ~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~  299 (385)
                      .-.+.+.|-...+...|++++.....   .|....+.|...|-+.|+-..|.+..            +..-+..-|....
T Consensus       561 l~qianiye~led~aqaie~~~q~~slip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtq  640 (840)
T KOG2003|consen  561 LVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQ  640 (840)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhH
Confidence            45566667777788999999877654   47788888999999999999998877            6677788888899


Q ss_pred             ChhhHHHHHHHHHhccc-hhhHHHHHHH-HHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCC
Q 040338          300 PVTKGKHYFTAMAKFTY-TCYFVCMVDL-LGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYN  364 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~-~~~~~~li~~-~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~  364 (385)
                      -+++++..|++..-..+ ..-|..+|.. +.+.|++..|..+|+..-++  .|..+...|++.+...|.
T Consensus       641 f~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  641 FSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            99999999999877766 6666666655 56699999999999998876  467788888888877764

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

Probab=99.14  E-value=1.7e-07  Score=80.22  Aligned_cols=265  Identities=11%  Similarity=-0.017  Sum_probs=193.6

Q ss_pred             hhhhHHHHHhhhCC---CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIGP---RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++.+|.++..+-.+   .....|-.-..+   ....|+.+.+-+++.+..+.--.++...+-+..+.....|+...|..-
T Consensus        99 ~~~qAEkl~~rnae~~e~p~l~~l~aA~A---A~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          99 DFQQAEKLLRRNAEHGEQPVLAYLLAAEA---AQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cHHHHHHHHHHhhhcCcchHHHHHHHHHH---HHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            78888888775442   223333333444   455899999999999998864456677777888889999999999998


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH-------hhHHHHH
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS-------MLYATAF  182 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-------~t~~~ll  182 (385)
                      +++..+.+                   +.++.+......+|.+.|++.....++..|.+.|+--|.       .+|..++
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-------------------PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLL  236 (400)
T ss_pred             HHHHHHhC-------------------cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHH
Confidence            88876555                   577889999999999999999999999999999865443       4566677


Q ss_pred             HHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC-
Q 040338          183 SARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR-  261 (385)
Q Consensus       183 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  261 (385)
                      .-....+..+.-...++..-+. .+.                      +...-.+++.-+..+|+.++|.++.++..+. 
T Consensus       237 ~q~~~~~~~~gL~~~W~~~pr~-lr~----------------------~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~  293 (400)
T COG3071         237 QQARDDNGSEGLKTWWKNQPRK-LRN----------------------DPELVVAYAERLIRLGDHDEAQEIIEDALKRQ  293 (400)
T ss_pred             HHHhccccchHHHHHHHhccHH-hhc----------------------ChhHHHHHHHHHHHcCChHHHHHHHHHHHHhc
Confidence            6666666655545555554333 112                      2233355667777888999999888776652 


Q ss_pred             -ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHH
Q 040338          262 -NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLL  327 (385)
Q Consensus       262 -~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~  327 (385)
                       |.. ... .-.+.+.++...-++..            .+.++...|.+.+.|.+|...|+...+..+ ...|+.+..++
T Consensus       294 ~D~~-L~~-~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~  371 (400)
T COG3071         294 WDPR-LCR-LIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADAL  371 (400)
T ss_pred             cChh-HHH-HHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHH
Confidence             333 111 11222333333332222            788999999999999999999999888888 99999999999


Q ss_pred             HccCCHHHHHHHHHhCC
Q 040338          328 GLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       328 ~~~g~~~~A~~~~~~m~  344 (385)
                      .+.|+..+|.++.++..
T Consensus       372 ~~~g~~~~A~~~r~e~L  388 (400)
T COG3071         372 DQLGEPEEAEQVRREAL  388 (400)
T ss_pred             HHcCChHHHHHHHHHHH
Confidence            99999999999988764

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.12  E-value=6.1e-09  Score=87.28  Aligned_cols=199  Identities=12%  Similarity=0.031  Sum_probs=153.6

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDM  219 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  219 (385)
                      ...+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|.+.++...+...             
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-------------   96 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNP-------------   96 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-------------
Confidence            4567788899999999999999999998752 33567778888899999999999999999887643             


Q ss_pred             HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccC
Q 040338          220 YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSG  299 (385)
Q Consensus       220 ~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~  299 (385)
                                .+...+..+...+...|++++|...++...+....              ....   -.+..+...+...|
T Consensus        97 ----------~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~--------------~~~~---~~~~~l~~~~~~~g  149 (234)
T TIGR02521        97 ----------NNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLY--------------PQPA---RSLENAGLCALKAG  149 (234)
T ss_pred             ----------CCHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccc--------------ccch---HHHHHHHHHHHHcC
Confidence                      22345688889999999999999999988642100              0000   02333445566777


Q ss_pred             ChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          300 PVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      ++++|...+++..+..+  ...+..+...+...|++++|.+.+++....  .+...+..+...+...|+.++|..+.+.+
T Consensus       150 ~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  229 (234)
T TIGR02521       150 DFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQL  229 (234)
T ss_pred             CHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            88888888888877766  667778899999999999999999987653  34566777888899999999999998888


Q ss_pred             Hhcc
Q 040338          376 LQLD  379 (385)
Q Consensus       376 ~~~~  379 (385)
                      ....
T Consensus       230 ~~~~  233 (234)
T TIGR02521       230 QKLF  233 (234)
T ss_pred             HhhC
Confidence            7653

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.11  E-value=1.9e-08  Score=84.27  Aligned_cols=189  Identities=14%  Similarity=0.062  Sum_probs=135.5

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ...+..+...+..   .|++++|.+.+++..+.. +.+...+..+...|...|++++|.+.+++..+.+           
T Consensus        31 ~~~~~~la~~~~~---~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-----------   95 (234)
T TIGR02521        31 AKIRVQLALGYLE---QGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-----------   95 (234)
T ss_pred             HHHHHHHHHHHHH---CCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-----------
Confidence            3455566666555   899999999999988764 3356778888889999999999999998876554           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                              +.+...+..+...+...|++++|...+++.......| ....+..+..++...|++++|.+.+++..+....
T Consensus        96 --------~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  167 (234)
T TIGR02521        96 --------PNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ  167 (234)
T ss_pred             --------CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC
Confidence                    3455677888888999999999999999988753223 3456666777888999999999999988876432


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchH
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~  283 (385)
                       +                      ...+..+...+...|++++|...+++..+  | +...+..+...+...|+.++|.
T Consensus       168 -~----------------------~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~  223 (234)
T TIGR02521       168 -R----------------------PESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQ  223 (234)
T ss_pred             -C----------------------hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHH
Confidence             1                      22345666777788899999999887754  2 3333444444444444444443

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.

>PRK12370 invasion protein regulator; Provisional

Probab=99.09  E-value=3.2e-08  Score=93.76  Aligned_cols=115  Identities=10%  Similarity=-0.203  Sum_probs=53.9

Q ss_pred             hHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHH
Q 040338           68 IKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMI  147 (385)
Q Consensus        68 ~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li  147 (385)
                      +++|...+++..+.. +-+...+..+...+...|++++|...|++..+.+                   +.+...+..+.
T Consensus       320 ~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-------------------P~~~~a~~~lg  379 (553)
T PRK12370        320 MIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-------------------PISADIKYYYG  379 (553)
T ss_pred             HHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHH
Confidence            455555555555442 2234444445455555555555555555544433                   23334455555


Q ss_pred             HHHHhCCCchHHHHHHHHHHHCCCCCCH-hhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          148 SILTRHGFGFETLCTFIELWNHGFGLSS-MLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       148 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      ..+...|++++|+..+++..+.  .|+. ..+..++..+...|++++|...+++..+.
T Consensus       380 ~~l~~~G~~~eAi~~~~~Al~l--~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~  435 (553)
T PRK12370        380 WNLFMAGQLEEALQTINECLKL--DPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQ  435 (553)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHh
Confidence            5555555555555555555543  2221 11122222333345555555555554443

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

Probab=99.09  E-value=2.6e-09  Score=99.48  Aligned_cols=248  Identities=12%  Similarity=-0.009  Sum_probs=167.6

Q ss_pred             HHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHh
Q 040338           73 HLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTR  152 (385)
Q Consensus        73 ~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~  152 (385)
                      .++..+...|+.|+..||..+|.-||..|+++.|- +|.-|.-++.                  +-+...|+.++.+..+
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksL------------------pv~e~vf~~lv~sh~~   71 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSL------------------PVREGVFRGLVASHKE   71 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccc------------------cccchhHHHHHhcccc
Confidence            56777888899999999999999999999999998 8888877665                  4567788889888888


Q ss_pred             CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh-------CCCCchHHHHHHHHHHHhcCC
Q 040338          153 HGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM-------EPSLDVFVGSGLIDMYLKCGC  225 (385)
Q Consensus       153 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~li~~~~~~g~  225 (385)
                      .++.+.+.           .|-..||..|..+|...||+..-..+-+.|...       |......-+-..+++     .
T Consensus        72 And~Enpk-----------ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c-----~  135 (1088)
T KOG4318|consen   72 ANDAENPK-----------EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHC-----C  135 (1088)
T ss_pred             cccccCCC-----------CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhccc-----C
Confidence            88877665           788889999999999998876532222223222       221111111111111     1


Q ss_pred             CCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC---------------ChhhHHHHHHHHHhcCCCCchHHHHHHHH
Q 040338          226 NGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR---------------NMISWMVLISAFSQAGVLEKPRFFFFFVS  290 (385)
Q Consensus       226 ~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---------------~~~~~~~li~~~~~~g~~~~a~~~~~~~~  290 (385)
                      ...-||.   .+.+.-....|-++.+++++..++..               +...+..|.. +|+.+.  ++....+|..
T Consensus       136 p~~lpda---~n~illlv~eglwaqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~-~cksl~--e~~~s~~l~a  209 (1088)
T KOG4318|consen  136 PHSLPDA---ENAILLLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLN-MCKSLV--EAPTSETLHA  209 (1088)
T ss_pred             cccchhH---HHHHHHHHHHHHHHHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHH-HHHHhh--cCCChHHHHH
Confidence            1122332   34455555666777777777666531               1112222222 222221  1333338899


Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---CCcchHHHHHHHHHhcCC
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---PTCVIWGALLGACCSHYN  364 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p~~~~~~~li~~~~~~g~  364 (385)
                      ++.+-..+|+.+.|..++.+|++.|+   ...|-.|+-+   .++..-++.+++.|.+.   |+..|+...+..+.+.|.
T Consensus       210 ~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  210 VLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             HHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            99999999999999999999999999   4445555554   88888888888888774   999999988888877544

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.07  E-value=6.1e-08  Score=88.34  Aligned_cols=246  Identities=13%  Similarity=0.048  Sum_probs=169.8

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHh-----c-cCCCch-HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccc
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKF-----Y-FVSDES-IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFG  124 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-----g-~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~  124 (385)
                      ...+-..|..   .|+++.|..+++...+.     | ..|... ..+.+...|...+++++|..+|+++...        
T Consensus       202 ~~~La~~y~~---~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i--------  270 (508)
T KOG1840|consen  202 LRNLAEMYAV---QGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTI--------  270 (508)
T ss_pred             HHHHHHHHHH---hccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH--------
Confidence            3335555444   99999999999998875     2 123332 3344667888899999999999775321        


Q ss_pred             hHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC-----CC-CCCHh-hHHHHHHHhcCccCccchhhH
Q 040338          125 IIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH-----GF-GLSSM-LYATAFSARASVYDLEWGPHL  197 (385)
Q Consensus       125 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----g~-~p~~~-t~~~ll~~~~~~~~~~~a~~~  197 (385)
                         -..+|.++.+.-..+++.|-..|.+.|++++|...+++..+.     |. .|... -++.+...|...+++++|..+
T Consensus       271 ---~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l  347 (508)
T KOG1840|consen  271 ---REEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKL  347 (508)
T ss_pred             ---HHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHH
Confidence               111222333334567888889999999999998888776432     32 33333 356677788999999999999


Q ss_pred             HHHHHHhC---CCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC-----------Ch
Q 040338          198 HSRVVHME---PSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR-----------NM  263 (385)
Q Consensus       198 ~~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----------~~  263 (385)
                      ++...+.-   +.++.                  ..-..+++.|...|.+.|++++|++++++....           ..
T Consensus       348 ~q~al~i~~~~~g~~~------------------~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~  409 (508)
T KOG1840|consen  348 LQKALKIYLDAPGEDN------------------VNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVG  409 (508)
T ss_pred             HHHHHHHHHhhccccc------------------hHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhh
Confidence            98766541   11211                  123457788999999999999999999988641           12


Q ss_pred             hhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHH
Q 040338          264 ISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLID  341 (385)
Q Consensus       264 ~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~  341 (385)
                      .+++.|...|.+.+++.+|.++|               .++..+........+  ..+|..|...|.+.|++++|.++.+
T Consensus       410 ~~l~~la~~~~~~k~~~~a~~l~---------------~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~  474 (508)
T KOG1840|consen  410 KPLNQLAEAYEELKKYEEAEQLF---------------EEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEE  474 (508)
T ss_pred             HHHHHHHHHHHHhcccchHHHHH---------------HHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHH
Confidence            45666777777777777777765               444444411111222  7788889999999999999999987


Q ss_pred             hCC
Q 040338          342 EMP  344 (385)
Q Consensus       342 ~m~  344 (385)
                      ...
T Consensus       475 ~~~  477 (508)
T KOG1840|consen  475 KVL  477 (508)
T ss_pred             HHH
Confidence            765

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.07  E-value=5e-07  Score=81.12  Aligned_cols=195  Identities=10%  Similarity=0.031  Sum_probs=128.4

Q ss_pred             ccccCCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHhhhCCCChhhHHHH--HHHHHhhhccCChHH
Q 040338            3 ACGSLKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFCDIGPRYLFTYNTM--INGGVRCLCVGNIKM   70 (385)
Q Consensus         3 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~~~~~~~~~~~~~l--i~~~~~~~~~~~~~~   70 (385)
                      -+...|++++|.++-..+...+..+.....          ++++|..+.+.-.  -..+++..  =.+||.+ +.+..++
T Consensus        21 ~~~~~~e~e~a~k~~~Kil~~~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~--~~~~~~~~~fEKAYc~Y-rlnk~De   97 (652)
T KOG2376|consen   21 RHGKNGEYEEAVKTANKILSIVPDDEDAIRCKVVALIQLDKYEDALKLIKKNG--ALLVINSFFFEKAYCEY-RLNKLDE   97 (652)
T ss_pred             HhccchHHHHHHHHHHHHHhcCCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcc--hhhhcchhhHHHHHHHH-HcccHHH
Confidence            356789999999999999998744433333          8999997766522  22233333  5677653 3699999


Q ss_pred             HHHHHHHHHHhccCCCc-hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccc----------cchHHHHHHhcCCCCCC
Q 040338           71 ALHLHGLVKKFYFVSDE-SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK----------FGIIRLLIMFQKMPERD  139 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~----------~~~~~a~~~~~~~~~~~  139 (385)
                      |+..++     |..++. .+...-...+-+.|++++|..+|+.+.+.+.....          +....+. +.+..+...
T Consensus        98 alk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~-~~q~v~~v~  171 (652)
T KOG2376|consen   98 ALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQ-LLQSVPEVP  171 (652)
T ss_pred             HHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHH-HHHhccCCC
Confidence            999887     344433 35556667888999999999999999776653333          1111111 344444434


Q ss_pred             cchHHHHHH---HHHhCCCchHHHHHHHHHHHCC-------------CCCCHhhH-HHHHHHhcCccCccchhhHHHHHH
Q 040338          140 LVSWNTMIS---ILTRHGFGFETLCTFIELWNHG-------------FGLSSMLY-ATAFSARASVYDLEWGPHLHSRVV  202 (385)
Q Consensus       140 ~~~~~~li~---~~~~~~~~~~a~~~~~~m~~~g-------------~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~  202 (385)
                      ..+|..+-+   .+...|++.+|+++++...+.|             +.-...+. ..+...+-..|+.++|..++...+
T Consensus       172 e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i  251 (652)
T KOG2376|consen  172 EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDII  251 (652)
T ss_pred             cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHH
Confidence            556665553   4567899999999999883221             11111222 234555678899999999999999


Q ss_pred             HhCC
Q 040338          203 HMEP  206 (385)
Q Consensus       203 ~~~~  206 (385)
                      +...
T Consensus       252 ~~~~  255 (652)
T KOG2376|consen  252 KRNP  255 (652)
T ss_pred             HhcC
Confidence            8865

>PRK12370 invasion protein regulator; Provisional

Probab=99.06  E-value=1.7e-08  Score=95.65  Aligned_cols=245  Identities=8%  Similarity=-0.075  Sum_probs=157.8

Q ss_pred             CchHHHhHHHHHHh-----cCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHH---------
Q 040338           86 DESIAKSSIDMHVK-----CGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILT---------  151 (385)
Q Consensus        86 ~~~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~---------  151 (385)
                      +...|...+++-..     .+.+++|...|++..+.+                   +.+...|..+..++.         
T Consensus       255 ~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ld-------------------P~~a~a~~~La~~~~~~~~~g~~~  315 (553)
T PRK12370        255 SIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMS-------------------PNSIAPYCALAECYLSMAQMGIFD  315 (553)
T ss_pred             ChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcC-------------------CccHHHHHHHHHHHHHHHHcCCcc
Confidence            44555555554322     134567778887776655                   234555665555443         


Q ss_pred             hCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCc
Q 040338          152 RHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIES  230 (385)
Q Consensus       152 ~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~  230 (385)
                      ..+++++|...+++..+.  .| +...+..+...+...|++++|...+++.++.++.                       
T Consensus       316 ~~~~~~~A~~~~~~Al~l--dP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~-----------------------  370 (553)
T PRK12370        316 KQNAMIKAKEHAIKATEL--DHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPI-----------------------  370 (553)
T ss_pred             cchHHHHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-----------------------
Confidence            234478999999998875  45 5667777777888899999999999999887632                       


Q ss_pred             hhhHHHHHHHHHHcCCChhHHHHHHHhccc--CCh-hhHHHHHHHHHhcCCCCchHHHH-------------HHHHHHHH
Q 040338          231 SIQIGKALVTMYAEGGSTQKADLAFELMSR--RNM-ISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSG  294 (385)
Q Consensus       231 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~-~~~~~li~~~~~~g~~~~a~~~~-------------~~~~l~~~  294 (385)
                      +...+..+...+...|++++|+..+++..+  |+. ..+..+...+...|++++|+..+             .+..+..+
T Consensus       371 ~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~  450 (553)
T PRK12370        371 SADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMF  450 (553)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHH
Confidence            223446667778888899999999998876  432 23333444566677777777666             34556666


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CCcchHHHHHHHHHhcCChHHH
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PTCVIWGALLGACCSHYNTKLA  368 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~~~~~~~li~~~~~~g~~~~a  368 (385)
                      +...|+.++|...+.++....+  ....+.+...|+..|  +.|...++.+.+.    |....+  +-..|.-.|+.+.+
T Consensus       451 l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~--~~~~~~~~g~~~~~  526 (553)
T PRK12370        451 LSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLESEQRIDNNPGL--LPLVLVAHGEAIAE  526 (553)
T ss_pred             HHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhhHhhcCchH--HHHHHHHHhhhHHH
Confidence            6778888888888877666555  444555566666666  4666666665542    333333  33335555666665


Q ss_pred             HHHHHHHHhcc
Q 040338          369 ELVMRNLLQLD  379 (385)
Q Consensus       369 ~~~~~~~~~~~  379 (385)
                      ..+ +++.+.+
T Consensus       527 ~~~-~~~~~~~  536 (553)
T PRK12370        527 KMW-NKFKNED  536 (553)
T ss_pred             HHH-HHhhccc
Confidence            555 7666554

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

Probab=99.04  E-value=2.7e-06  Score=77.52  Aligned_cols=297  Identities=10%  Similarity=0.028  Sum_probs=140.4

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhc----cCCCccccccchHHHHHHhcCCCCCCc
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRM----LNPSLFCWKFGIIRLLIMFQKMPERDL  140 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m----~~~~~~~~~~~~~~a~~~~~~~~~~~~  140 (385)
                      ..-++.|.++++...+. ++-+..+|.+-...=-.+|+.+.+.++.++-    ...|+                  .-+.
T Consensus       419 LetYenAkkvLNkaRe~-iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv------------------~i~r  479 (913)
T KOG0495|consen  419 LETYENAKKVLNKAREI-IPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGV------------------EINR  479 (913)
T ss_pred             HHHHHHHHHHHHHHHhh-CCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcce------------------eecH
Confidence            56666777777766654 4556666666666556667777776666543    12222                  2233


Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC--HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLS--SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLID  218 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  218 (385)
                      ..|-.=...|-..|..--+..+......-|+.-.  ..|+..-...|.+.+.++-|..+|...++- ++.+..+|.....
T Consensus       480 dqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~  558 (913)
T KOG0495|consen  480 DQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAM  558 (913)
T ss_pred             HHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHH
Confidence            3333333334444444444444444444443321  234444444444445555555555444443 2223333333322


Q ss_pred             HHHhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchH
Q 040338          219 MYLKCGCNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       219 ~~~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~  283 (385)
                      .--..|..+            ++.....|-.....+-..|++..|..++....+  | +...|-.-+..-.....+++|.
T Consensus       559 ~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR  638 (913)
T KOG0495|consen  559 FEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERAR  638 (913)
T ss_pred             HHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHH
Confidence            222222111            223333444444555555666666666665544  2 3344555555555555666666


Q ss_pred             HHH-----------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCc
Q 040338          284 FFF-----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTC  349 (385)
Q Consensus       284 ~~~-----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~  349 (385)
                      .+|           .|..-+..---.++.++|.+++++..+..+  ...|..+.+.+-+.++++.|.+.|..=... |+.
T Consensus       639 ~llakar~~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~  718 (913)
T KOG0495|consen  639 DLLAKARSISGTERVWMKSANLERYLDNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNS  718 (913)
T ss_pred             HHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCC
Confidence            665           333333333444555666666665555555  455555555555555555555544433322 322


Q ss_pred             c-hHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          350 V-IWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       350 ~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      . .|-.|...--+.|..-+|..++++..-.+|+
T Consensus       719 ipLWllLakleEk~~~~~rAR~ildrarlkNPk  751 (913)
T KOG0495|consen  719 IPLWLLLAKLEEKDGQLVRARSILDRARLKNPK  751 (913)
T ss_pred             chHHHHHHHHHHHhcchhhHHHHHHHHHhcCCC
Confidence            2 3333333333444444444444444444433

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

Probab=99.04  E-value=2e-06  Score=78.39  Aligned_cols=291  Identities=11%  Similarity=0.031  Sum_probs=191.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|..++...++++.+..- +-....|-.....+...|++..|..++.+.-+.+                   +.+...|-
T Consensus       563 hgt~Esl~Allqkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~-------------------pnseeiwl  622 (913)
T KOG0495|consen  563 HGTRESLEALLQKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEAN-------------------PNSEEIWL  622 (913)
T ss_pred             cCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhC-------------------CCcHHHHH
Confidence            455555555555555431 2223333333444444555555555555443333                   23667788


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      +-+..-..+.+++.|..+|.+...  ..|+...|.--++.-.-.+..++|.+++++.++.- +.=...|-.+-..+-+.+
T Consensus       623 aavKle~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~f-p~f~Kl~lmlGQi~e~~~  699 (913)
T KOG0495|consen  623 AAVKLEFENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEALRLLEEALKSF-PDFHKLWLMLGQIEEQME  699 (913)
T ss_pred             HHHHHhhccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhC-CchHHHHHHHhHHHHHHH
Confidence            888888888889999988888765  56777777666666666778888888888887763 222334433333343333


Q ss_pred             CCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH---
Q 040338          225 CNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF---  286 (385)
Q Consensus       225 ~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~---  286 (385)
                      +.+            ++..+..|-.|.+.--+.|.+-.|..+++.-.-  | |...|-..|..=.+.|..+.|..+.   
T Consensus       700 ~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakA  779 (913)
T KOG0495|consen  700 NIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKA  779 (913)
T ss_pred             HHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            333            566677777777777788888888888886653  3 5678888888888888888887666   


Q ss_pred             ---------HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHH
Q 040338          287 ---------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGA  354 (385)
Q Consensus       287 ---------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~  354 (385)
                               .|...|....+.++-.++..-++   +... +.+...+...+-...+++.|.+.|++.... | +..+|.-
T Consensus       780 LQecp~sg~LWaEaI~le~~~~rkTks~DALk---kce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~  856 (913)
T KOG0495|consen  780 LQECPSSGLLWAEAIWLEPRPQRKTKSIDALK---KCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAW  856 (913)
T ss_pred             HHhCCccchhHHHHHHhccCcccchHHHHHHH---hccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHH
Confidence                     45555555444444333333222   2222 555666667777788899999999988764 4 4668999


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          355 LLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       355 li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      +...+..+|.-+.-.++++......|.
T Consensus       857 fykfel~hG~eed~kev~~~c~~~EP~  883 (913)
T KOG0495|consen  857 FYKFELRHGTEEDQKEVLKKCETAEPT  883 (913)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhccCCC
Confidence            999999999888888898888876664

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

Probab=99.04  E-value=8.3e-09  Score=85.82  Aligned_cols=210  Identities=12%  Similarity=0.011  Sum_probs=156.9

Q ss_pred             HhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCC
Q 040338           91 KSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHG  170 (385)
Q Consensus        91 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  170 (385)
                      +.+..+|.+.|.+.+|.+.|+.-.+.                    .|-+.||-.|-..|.+-.+++.|+.+|.+-.+. 
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--------------------~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-  285 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--------------------FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-  285 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--------------------CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-
Confidence            56778999999999999998775443                    366678989999999999999999999988764 


Q ss_pred             CCCCHhhH-HHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChh
Q 040338          171 FGLSSMLY-ATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQ  249 (385)
Q Consensus       171 ~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~  249 (385)
                       -|-.+|| .-+.+.+-..++.++|.++++...+...                       .++....++...|.-.++.+
T Consensus       286 -fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~~-----------------------~nvEaiAcia~~yfY~~~PE  341 (478)
T KOG1129|consen  286 -FPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLHP-----------------------INVEAIACIAVGYFYDNNPE  341 (478)
T ss_pred             -CCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcCC-----------------------ccceeeeeeeeccccCCChH
Confidence             5656665 4577788889999999999999988743                       23444456667788888999


Q ss_pred             HHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH---------------HHHHHHHHhcccCChhhHHHHHHHH
Q 040338          250 KADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF---------------FFVSLLSGCSHSGPVTKGKHYFTAM  311 (385)
Q Consensus       250 ~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~---------------~~~~l~~~~~~~~~~~~a~~~~~~~  311 (385)
                      -|+..|..+.+   .+...|+.+.-.|.-.+++|-++--|               .|-++-......||...|.+.|.-.
T Consensus       342 ~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrla  421 (478)
T KOG1129|consen  342 MALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLA  421 (478)
T ss_pred             HHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHH
Confidence            99999998876   46778888888887888887776555               5555555556666666666666666


Q ss_pred             Hhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          312 AKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       312 ~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ...+.  ...++.|.-.-.+.|++++|..++.....
T Consensus       422 L~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s  457 (478)
T KOG1129|consen  422 LTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKS  457 (478)
T ss_pred             hccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhh
Confidence            55555  55666666666666666666666665554

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.94  E-value=2.9e-07  Score=80.80  Aligned_cols=192  Identities=9%  Similarity=-0.015  Sum_probs=118.4

Q ss_pred             hcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHH
Q 040338          185 RASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------------IESSIQIGKALVTMYAEGGSTQKAD  252 (385)
Q Consensus       185 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~  252 (385)
                      +.-.|+.-.+..-|+..+.....++.. |-.+..+|....+..            .+.+..+|..=..++.-.+++++|.
T Consensus       336 ~fL~g~~~~a~~d~~~~I~l~~~~~~l-yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~  414 (606)
T KOG0547|consen  336 HFLKGDSLGAQEDFDAAIKLDPAFNSL-YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAI  414 (606)
T ss_pred             hhhcCCchhhhhhHHHHHhcCcccchH-HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHH
Confidence            344566666666666666654443331 333333333333222            3344455555556666666778888


Q ss_pred             HHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-
Q 040338          253 LAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-  316 (385)
Q Consensus       253 ~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-  316 (385)
                      .=|++-+.-   ++..|--+--+..+.++++++...|            .|+...+.+...++++.|.+.|+......+ 
T Consensus       415 aDF~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~  494 (606)
T KOG0547|consen  415 ADFQKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPR  494 (606)
T ss_pred             HHHHHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccc
Confidence            878777652   4455655666666777777777777            788888888888888888888887766544 


Q ss_pred             --------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          317 --------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       317 --------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                              .+...--+-.+--.+++..|.++++...+- | ....|.+|...-...|+.++|+++|++...
T Consensus       495 ~~~~~v~~~plV~Ka~l~~qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  495 EHLIIVNAAPLVHKALLVLQWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             cccccccchhhhhhhHhhhchhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                    111111111222347778888888777663 3 344678888888888888888888877543

>PF12854 PPR_1: PPR repeat

Probab=98.94  E-value=1.2e-09  Score=60.34  Aligned_cols=34  Identities=29%  Similarity=0.109  Sum_probs=30.7

Q ss_pred             hccCCCchHHHhHHHHHHhcCChhHHHHHHHhcc
Q 040338           81 FYFVSDESIAKSSIDMHVKCGAVDYAESAFLRML  114 (385)
Q Consensus        81 ~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  114 (385)
                      +|+.||..+||+||++||+.|++++|.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            4789999999999999999999999999999884

>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=98.91  E-value=1.6e-06  Score=80.12  Aligned_cols=272  Identities=13%  Similarity=0.046  Sum_probs=147.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|++.++.-.+. +.............+.+.|+.++|..+|..+.+.|                   +.|..-|.
T Consensus        17 ~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN-------------------Pdn~~Yy~   76 (517)
T PF12569_consen   17 AGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN-------------------PDNYDYYR   76 (517)
T ss_pred             CCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-------------------CCcHHHHH
Confidence            78888888888765443 33344556667788888888888888888887776                   23444444


Q ss_pred             HHHHHHHhC-----CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCc-cchhhHHHHHHHhCCCCc---------
Q 040338          145 TMISILTRH-----GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDL-EWGPHLHSRVVHMEPSLD---------  209 (385)
Q Consensus       145 ~li~~~~~~-----~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~~~~~~~~~~---------  209 (385)
                      .+..+....     ...+....+|+++...  -|.......+.-.+.....+ ..+...+..+.+.|+++-         
T Consensus        77 ~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~--yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~  154 (517)
T PF12569_consen   77 GLEEALGLQLQLSDEDVEKLLELYDELAEK--YPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYK  154 (517)
T ss_pred             HHHHHHhhhcccccccHHHHHHHHHHHHHh--CccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHc
Confidence            454444222     2456667777777654  23333332222122221122 123344444555554221         


Q ss_pred             ----hHHHHHHHHHHHhcC----CC-------CCCchhhHH--HHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHH
Q 040338          210 ----VFVGSGLIDMYLKCG----CN-------GIESSIQIG--KALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISA  272 (385)
Q Consensus       210 ----~~~~~~li~~~~~~g----~~-------~~~~~~~~~--~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~  272 (385)
                          ..+.-.++..|...-    ..       .-+|+...|  ..+...|-..|++++|++++++..+.++..    ++ 
T Consensus       155 d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~----~e-  229 (517)
T PF12569_consen  155 DPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTL----VE-  229 (517)
T ss_pred             ChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCc----HH-
Confidence                111112222222111    00       012333222  333444445555555555555444321110    00 


Q ss_pred             HHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCCC---
Q 040338          273 FSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKP---  347 (385)
Q Consensus       273 ~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p---  347 (385)
                                    .|..-...+.+.|++.+|...++.....+.  ...-+-.+..+.++|++++|.+++.......   
T Consensus       230 --------------ly~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~  295 (517)
T PF12569_consen  230 --------------LYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDP  295 (517)
T ss_pred             --------------HHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCc
Confidence                          344444555667777777788888777777  5555567777888888888888887765531   


Q ss_pred             Ccc------hH--HHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          348 TCV------IW--GALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       348 ~~~------~~--~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      -..      .|  .....+|.+.|++..|++.|..+.+
T Consensus       296 ~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  296 LSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            111      11  3356778888888888777766543

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 [], [].

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

Probab=98.87  E-value=6.7e-06  Score=74.88  Aligned_cols=340  Identities=14%  Similarity=0.114  Sum_probs=198.9

Q ss_pred             hhhhHHHHHhhhC-----CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHH
Q 040338           33 LIDDDYRVFCDIG-----PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAE  107 (385)
Q Consensus        33 ~~~~A~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~  107 (385)
                      ++-..++.|++..     ......|.-.|.-...   .+-++-+.++++.-.+.    ++..-+-.|..+++.+++++|.
T Consensus       117 ~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~---~~lPets~rvyrRYLk~----~P~~~eeyie~L~~~d~~~eaa  189 (835)
T KOG2047|consen  117 LITRTRRTFDRALRALPVTQHDRIWDLYLKFVES---HGLPETSIRVYRRYLKV----APEAREEYIEYLAKSDRLDEAA  189 (835)
T ss_pred             hHHHHHHHHHHHHHhCchHhhccchHHHHHHHHh---CCChHHHHHHHHHHHhc----CHHHHHHHHHHHHhccchHHHH
Confidence            5556666666433     2234567777766444   78888999999888763    4444677888999999999999


Q ss_pred             HHHHhccCCCccccc------cchHHHHH----------------HhcCCCC--CC--cchHHHHHHHHHhCCCchHHHH
Q 040338          108 SAFLRMLNPSLFCWK------FGIIRLLI----------------MFQKMPE--RD--LVSWNTMISILTRHGFGFETLC  161 (385)
Q Consensus       108 ~~~~~m~~~~~~~~~------~~~~~a~~----------------~~~~~~~--~~--~~~~~~li~~~~~~~~~~~a~~  161 (385)
                      +.+......+.+.-.      .-+.+--+                ++..+..  +|  ...|++|.+.|.+.|.+++|-+
T Consensus       190 ~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarD  269 (835)
T KOG2047|consen  190 QRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARD  269 (835)
T ss_pred             HHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            999888655432211      11111111                1111111  22  2358999999999999999999


Q ss_pred             HHHHHHHCCCCCCHhhHHHHHHHhcCccC----------------------ccchhhHHHHHHHhCC-----------CC
Q 040338          162 TFIELWNHGFGLSSMLYATAFSARASVYD----------------------LEWGPHLHSRVVHMEP-----------SL  208 (385)
Q Consensus       162 ~~~~m~~~g~~p~~~t~~~ll~~~~~~~~----------------------~~~a~~~~~~~~~~~~-----------~~  208 (385)
                      +|++....  ..+..-|+.+.++|..-..                      ++....-|+.+...++           +.
T Consensus       270 vyeeai~~--v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLRQn~~  347 (835)
T KOG2047|consen  270 VYEEAIQT--VMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLLRQNPH  347 (835)
T ss_pred             HHHHHHHh--heehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHHhcCCc
Confidence            99998764  3455556666666543211                      1111122222222211           01


Q ss_pred             chHHHHHHHHHHHhcC--------------CCC--CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChh-------h
Q 040338          209 DVFVGSGLIDMYLKCG--------------CNG--IESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMI-------S  265 (385)
Q Consensus       209 ~~~~~~~li~~~~~~g--------------~~~--~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~-------~  265 (385)
                      ++..|..-+..+-...              ++.  +..-...|..+.+.|-..|+++.|..+|++..+-+-.       +
T Consensus       348 nV~eW~kRV~l~e~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~v  427 (835)
T KOG2047|consen  348 NVEEWHKRVKLYEGNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEV  427 (835)
T ss_pred             cHHHHHhhhhhhcCChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHH
Confidence            1111111111111000              000  2222456778888899999999999999988763222       2


Q ss_pred             HHHHHHHHHhcCCCCchHHHH------------------------------HHHHHHHHhcccCChhhHHHHHHHHHhcc
Q 040338          266 WMVLISAFSQAGVLEKPRFFF------------------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFT  315 (385)
Q Consensus       266 ~~~li~~~~~~g~~~~a~~~~------------------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  315 (385)
                      |..-.+.=.++.+++.|+.+.                              .|...++.--..|-++....+++++....
T Consensus       428 w~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLr  507 (835)
T KOG2047|consen  428 WCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLR  507 (835)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHh
Confidence            333333333445556666555                              55555555556678888888888888876


Q ss_pred             c--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---CCcc-hHHHHHHHHHh---cCChHHHHHHHHHHHhccccC
Q 040338          316 Y--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---PTCV-IWGALLGACCS---HYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       316 ~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p~~~-~~~~li~~~~~---~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .  +.+.....-.+-...-++++.++|++-..-   |++. .|++.+.-+.+   ....+.|..+|++.++ +++|
T Consensus       508 iaTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp  582 (835)
T KOG2047|consen  508 IATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPP  582 (835)
T ss_pred             cCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCH
Confidence            6  333333333444556678888888877652   5543 46655544333   3467889999999888 4433

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.85  E-value=1.1e-06  Score=76.42  Aligned_cols=228  Identities=11%  Similarity=-0.026  Sum_probs=139.8

Q ss_pred             cCChHHHHHHHHHHHHhcc-CCC--chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcc
Q 040338           65 VGNIKMALHLHGLVKKFYF-VSD--ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLV  141 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~-~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~  141 (385)
                      .+..+.++.-+.++..... .|+  ...|..+...|.+.|+.++|...|++..+.+                   +.+..
T Consensus        39 ~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-------------------P~~~~   99 (296)
T PRK11189         39 TLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR-------------------PDMAD   99 (296)
T ss_pred             chHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-------------------CCCHH
Confidence            3555677777777775421 222  3457777778888899999988888876655                   35677


Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      .|+.+...+...|++++|...|++..+.  .| +..++..+..++...|++++|.+.++...+..+...  ..       
T Consensus       100 a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~--~~-------  168 (296)
T PRK11189        100 AYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDP--YR-------  168 (296)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH--HH-------
Confidence            8888888999999999999999888864  55 356677777778888999999999988887653211  00       


Q ss_pred             HhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccC
Q 040338          221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSG  299 (385)
Q Consensus       221 ~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~  299 (385)
                                     ..........++.++|...|++.... +...|. ........|+..++. .+  ..+..+     
T Consensus       169 ---------------~~~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~-~~~~~~~lg~~~~~~-~~--~~~~~~-----  224 (296)
T PRK11189        169 ---------------ALWLYLAESKLDPKQAKENLKQRYEKLDKEQWG-WNIVEFYLGKISEET-LM--ERLKAG-----  224 (296)
T ss_pred             ---------------HHHHHHHHccCCHHHHHHHHHHHHhhCCccccH-HHHHHHHccCCCHHH-HH--HHHHhc-----
Confidence                           11111223456788888888654332 222222 122223344443321 10  011110     


Q ss_pred             ChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHH
Q 040338          300 PVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGA  354 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~  354 (385)
                              ++...+.+.  ...|.-+...+.+.|++++|...|++....  ||.+-+..
T Consensus       225 --------~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~~~~~e~~~  275 (296)
T PRK11189        225 --------ATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNVYNFVEHRY  275 (296)
T ss_pred             --------CCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCchHHHHHH
Confidence                    000011111  456777778888888888888888877653  35444444

>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=98.85  E-value=3.4e-06  Score=77.99  Aligned_cols=227  Identities=7%  Similarity=-0.121  Sum_probs=141.3

Q ss_pred             hhhhHHHHHhhhC--CCChhhHH-HHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhc-----CChh
Q 040338           33 LIDDDYRVFCDIG--PRYLFTYN-TMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKC-----GAVD  104 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~~~~-~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-----g~~~  104 (385)
                      ++++|...++.-.  -+|..+|. ..-..+.+   .|+.++|..++..+.+.+. .|..-|..+..+..-.     ...+
T Consensus        19 ~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~k---Lg~~~eA~~~y~~Li~rNP-dn~~Yy~~L~~~~g~~~~~~~~~~~   94 (517)
T PF12569_consen   19 DYEEALEHLEKNEKQILDKLAVLEKRAELLLK---LGRKEEAEKIYRELIDRNP-DNYDYYRGLEEALGLQLQLSDEDVE   94 (517)
T ss_pred             CHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHhhhcccccccHH
Confidence            6777777776544  45655554 44444444   8999999999999999862 2444455555555332     2467


Q ss_pred             HHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCch-HHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040338          105 YAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGF-ETLCTFIELWNHGFGLSSMLYATAFS  183 (385)
Q Consensus       105 ~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~-~a~~~~~~m~~~g~~p~~~t~~~ll~  183 (385)
                      ...++|+++....+                    ...+.-.+.-.+.....+. .+..++..+...|+++   +|+.|-.
T Consensus        95 ~~~~~y~~l~~~yp--------------------~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~  151 (517)
T PF12569_consen   95 KLLELYDELAEKYP--------------------RSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKP  151 (517)
T ss_pred             HHHHHHHHHHHhCc--------------------cccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHH
Confidence            77788887754432                    1111111111111112232 4556667777788654   4555555


Q ss_pred             HhcCccCccchhhHHHHHHHhC--------------CCCchH--HHHHHHHHHHhcCCCC-----------CCch-hhHH
Q 040338          184 ARASVYDLEWGPHLHSRVVHME--------------PSLDVF--VGSGLIDMYLKCGCNG-----------IESS-IQIG  235 (385)
Q Consensus       184 ~~~~~~~~~~a~~~~~~~~~~~--------------~~~~~~--~~~~li~~~~~~g~~~-----------~~~~-~~~~  235 (385)
                      .|.......-..+++.......              -.|+..  ++.-+...|...|+.+           ..|+ +..|
T Consensus       152 Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely  231 (517)
T PF12569_consen  152 LYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELY  231 (517)
T ss_pred             HHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHH
Confidence            5665555555556666555331              124443  3455567788888777           5555 6788


Q ss_pred             HHHHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH
Q 040338          236 KALVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF  286 (385)
Q Consensus       236 ~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~  286 (385)
                      ..-.+.+-+.|++.+|.+.++...+-   |-..-+-.+..+.++|+.++|.+++
T Consensus       232 ~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~  285 (517)
T PF12569_consen  232 MTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTA  285 (517)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            88899999999999999999988764   4445555666677777777776654

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 [], [].

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

Probab=98.83  E-value=5.6e-06  Score=74.27  Aligned_cols=254  Identities=9%  Similarity=-0.056  Sum_probs=117.8

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +......-.+-+-..+++++..++++...+.+                   +++...+-.=|.++...|+..+-..+=.+
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-------------------pfh~~~~~~~ia~l~el~~~n~Lf~lsh~  303 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEKD-------------------PFHLPCLPLHIACLYELGKSNKLFLLSHK  303 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-------------------CCCcchHHHHHHHHHHhcccchHHHHHHH
Confidence            34444444445555566666666666655544                   34445555555566666665555555555


Q ss_pred             HHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------------CCchhh
Q 040338          166 LWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------------IESSIQ  233 (385)
Q Consensus       166 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------------~~~~~~  233 (385)
                      |.+. .+-...+|-.+.--|...|...+|.+.|.........-. ..|-..-+.|.-.|..+            .+....
T Consensus       304 LV~~-yP~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fg-paWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hl  381 (611)
T KOG1173|consen  304 LVDL-YPSKALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFG-PAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHL  381 (611)
T ss_pred             HHHh-CCCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCcccc-HHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcc
Confidence            5543 222445555555555555666666666665544322110 11111111111111000            000000


Q ss_pred             HHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHH
Q 040338          234 IGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTA  310 (385)
Q Consensus       234 ~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~  310 (385)
                      -+--+.--|.+.++++.|.+.|.....  | |+...+.+.-.....+.+.+|.                      ..|+.
T Consensus       382 P~LYlgmey~~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~----------------------~~f~~  439 (611)
T KOG1173|consen  382 PSLYLGMEYMRTNNLKLAEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEAL----------------------KYFQK  439 (611)
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHH----------------------HHHHH
Confidence            001122334444555555555544432  2 3334444433333444444444                      44443


Q ss_pred             HHhc----cc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          311 MAKF----TY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       311 ~~~~----~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      ....    +.     .++++-|..+|.+.+++++|+..++.....  .+..+|.++.-.|...|+++.|...|.+.+-..
T Consensus       440 ~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~  519 (611)
T KOG1173|consen  440 ALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALK  519 (611)
T ss_pred             HHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcC
Confidence            3310    00     344555566666666666666666555442  345555555555666666666666666555554


Q ss_pred             ccC
Q 040338          380 VKV  382 (385)
Q Consensus       380 ~~~  382 (385)
                      |.+
T Consensus       520 p~n  522 (611)
T KOG1173|consen  520 PDN  522 (611)
T ss_pred             Ccc
Confidence            443

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

Probab=98.81  E-value=8.9e-08  Score=79.82  Aligned_cols=214  Identities=7%  Similarity=-0.080  Sum_probs=177.2

Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      +-+-.+|.+.|.+.+|.+.|+.-.+.  .|-..||..|-+.|.+..+.+.|+.++.+-++.-  |-.+||          
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f--P~~VT~----------  292 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF--PFDVTY----------  292 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC--Cchhhh----------
Confidence            45788999999999999999988775  6777889999999999999999999999887752  333332          


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH------------HH
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF------------FF  288 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~------------~~  288 (385)
                                 ..-+.+.+-..++.++|.++|+...+.   ++.....+...|.-.++++-|+.++            .|
T Consensus       293 -----------l~g~ARi~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf  361 (478)
T KOG1129|consen  293 -----------LLGQARIHEAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELF  361 (478)
T ss_pred             -----------hhhhHHHHHHHHhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHH
Confidence                       344556666677999999999988763   5666666777888899999999988            89


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHh
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCS  361 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~  361 (385)
                      +++.-+|.-.++++.+..-|.+....-.     ..+|-.+.....-.|++..|.+-|+-....  .+...++.|.-.-.+
T Consensus       362 ~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r  441 (478)
T KOG1129|consen  362 CNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAAR  441 (478)
T ss_pred             hhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhh
Confidence            9999999999999999999988765333     777877888888999999999999887764  456789999998999


Q ss_pred             cCChHHHHHHHHHHHhccccC
Q 040338          362 HYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       362 ~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .|+.++|..++....+..|.-
T Consensus       442 ~G~i~~Arsll~~A~s~~P~m  462 (478)
T KOG1129|consen  442 SGDILGARSLLNAAKSVMPDM  462 (478)
T ss_pred             cCchHHHHHHHHHhhhhCccc
Confidence            999999999999998877753

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.79  E-value=9.9e-06  Score=73.10  Aligned_cols=115  Identities=12%  Similarity=0.026  Sum_probs=62.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCC---Cccccc--------
Q 040338           54 TMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNP---SLFCWK--------  122 (385)
Q Consensus        54 ~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~~~~--------  122 (385)
                      .++.-+.+....+++++|.+....+...+ +-+...+..=+-++.+.+++++|+.+.+.-...   +.+.+.        
T Consensus        14 ~l~t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~~~~~~~fEKAYc~Yrl   92 (652)
T KOG2376|consen   14 ALLTDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGALLVINSFFFEKAYCEYRL   92 (652)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhhhcchhhHHHHHHHHHc
Confidence            44444445555777888888887777765 334555566666677777788877665432210   111001        


Q ss_pred             cchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          123 FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       123 ~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      +..++|++.+..+.+.|..+-..-...+.+.|++++|+++|+.+.+.
T Consensus        93 nk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn  139 (652)
T KOG2376|consen   93 NKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKN  139 (652)
T ss_pred             ccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            44444444444333333334444445555666666666666666554

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.75  E-value=6.4e-07  Score=78.75  Aligned_cols=138  Identities=12%  Similarity=0.053  Sum_probs=102.1

Q ss_pred             cCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHH
Q 040338          244 EGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      -.|+.-.|..-|+..++  | +...|--+...|....+..+-...|            +|..-.....-.+++++|..=|
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF  417 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADF  417 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCcccchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHH
Confidence            34556666666665554  1 2233555666677777666666666            6666666677777788888888


Q ss_pred             HHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          309 TAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       309 ~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ++.....+  ...|..+..+.-+.+++++++..|++.+.+ |+ +..|+.+...+...++++.|.+.|+..+++.+.
T Consensus       418 ~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~  494 (606)
T KOG0547|consen  418 QKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPR  494 (606)
T ss_pred             HHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccc
Confidence            88877777  555666666777888999999999999887 65 457899999999999999999999999888776

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.75  E-value=2.4e-06  Score=74.39  Aligned_cols=194  Identities=10%  Similarity=-0.039  Sum_probs=117.0

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDM  219 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  219 (385)
                      ..|..+...|...|++++|...|++..+.  .| +...|+.+...+...|++++|...|+..++..+  +          
T Consensus        65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P--~----------  130 (296)
T PRK11189         65 QLHYERGVLYDSLGLRALARNDFSQALAL--RPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDP--T----------  130 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--C----------
Confidence            34566666667777777777777776664  33 456666677777777777777777777766432  1          


Q ss_pred             HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhh-HHHHHHHHHhcCCCCchHHHHHHHHHHHHhccc
Q 040338          220 YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMIS-WMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHS  298 (385)
Q Consensus       220 ~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~-~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~  298 (385)
                                 +..+|..+...+...|++++|.+.|+...+.+... +..+                  |   ...+...
T Consensus       131 -----------~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~------------------~---~~l~~~~  178 (296)
T PRK11189        131 -----------YNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRAL------------------W---LYLAESK  178 (296)
T ss_pred             -----------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH------------------H---HHHHHcc
Confidence                       23345666667777777777777776665421111 1110                  0   0112234


Q ss_pred             CChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCC---CC-----C-CcchHHHHHHHHHhcCChHHHH
Q 040338          299 GPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMP---SK-----P-TCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       299 ~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~-----p-~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      ++.++|...+++.........+. ........|+.+++ +.++.+.   +.     | ....|..+...+...|++++|.
T Consensus       179 ~~~~~A~~~l~~~~~~~~~~~~~-~~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~  256 (296)
T PRK11189        179 LDPKQAKENLKQRYEKLDKEQWG-WNIVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAA  256 (296)
T ss_pred             CCHHHHHHHHHHHHhhCCccccH-HHHHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Confidence            56788888886654432322222 22333345555443 2333332   21     1 2357899999999999999999


Q ss_pred             HHHHHHHhccccC
Q 040338          370 LVMRNLLQLDVKV  382 (385)
Q Consensus       370 ~~~~~~~~~~~~~  382 (385)
                      ..|++..+.+|.+
T Consensus       257 ~~~~~Al~~~~~~  269 (296)
T PRK11189        257 ALFKLALANNVYN  269 (296)
T ss_pred             HHHHHHHHhCCch
Confidence            9999999988754

>PF12854 PPR_1: PPR repeat

Probab=98.68  E-value=2.1e-08  Score=55.39  Aligned_cols=31  Identities=32%  Similarity=0.349  Sum_probs=28.7

Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      +||..|||+||.+||+.|+.++|.++|++|.
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            7999999999999999999999999999984

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.68  E-value=3.3e-06  Score=78.00  Aligned_cols=129  Identities=11%  Similarity=0.081  Sum_probs=90.4

Q ss_pred             HHHHHcCCChhHHHHHHHhcccCCh--hhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHH
Q 040338          239 VTMYAEGGSTQKADLAFELMSRRNM--ISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMA  312 (385)
Q Consensus       239 i~~~~~~g~~~~A~~~~~~m~~~~~--~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~  312 (385)
                      +.+-.....|.+|+.+++.+++.++  .-|..+...|...|+++.|.++|    .++-.|..|.+.|+|+.|.++-++..
T Consensus       739 ieaai~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~~~~dai~my~k~~kw~da~kla~e~~  818 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEADLFKDAIDMYGKAGKWEDAFKLAEECH  818 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcchhHHHHHHHhccccHHHHHHHHHHhc
Confidence            3444556788899999998887654  34677888999999999999999    88999999999999999999877754


Q ss_pred             hccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHH
Q 040338          313 KFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMR  373 (385)
Q Consensus       313 ~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  373 (385)
                      .... ...|.+-..-+-+.|++.+|.++|-.+.+ |+.     .|..|-++|..+..+++.+
T Consensus       819 ~~e~t~~~yiakaedldehgkf~eaeqlyiti~~-p~~-----aiqmydk~~~~ddmirlv~  874 (1636)
T KOG3616|consen  819 GPEATISLYIAKAEDLDEHGKFAEAEQLYITIGE-PDK-----AIQMYDKHGLDDDMIRLVE  874 (1636)
T ss_pred             CchhHHHHHHHhHHhHHhhcchhhhhheeEEccC-chH-----HHHHHHhhCcchHHHHHHH
Confidence            4333 55555555566677777777777655443 221     3444444444444444443

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

Probab=98.66  E-value=9.3e-05  Score=67.72  Aligned_cols=95  Identities=15%  Similarity=0.213  Sum_probs=64.7

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHHHhCCCCC-------------
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKP-------------  347 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p-------------  347 (385)
                      .|..+...|-..|+++.|+.+|++..+.+.      ..+|....++-.+..+++.|.++.+....-|             
T Consensus       389 Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~p  468 (835)
T KOG2047|consen  389 LWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEP  468 (835)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCc
Confidence            667777777778888888888888777665      4555556666667777788887777664421             


Q ss_pred             -------CcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          348 -------TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       348 -------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                             +...|+..+...-..|-++....++++++++.+.
T Consensus       469 vQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLria  509 (835)
T KOG2047|consen  469 VQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIA  509 (835)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcC
Confidence                   1234556666666667777777777777776654

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

Probab=98.65  E-value=3.2e-05  Score=69.54  Aligned_cols=256  Identities=12%  Similarity=-0.080  Sum_probs=154.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh----cCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC-
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK----CGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD-  139 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~-  139 (385)
                      .|++++|.+.++...+.. +.+...+.. ...+..    .+....+.+.++.. .+.                   .|+ 
T Consensus        56 ~g~~~~A~~~~~~~l~~~-P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~~-~~~-------------------~~~~  113 (355)
T cd05804          56 AGDLPKALALLEQLLDDY-PRDLLALKL-HLGAFGLGDFSGMRDHVARVLPLW-APE-------------------NPDY  113 (355)
T ss_pred             cCCHHHHHHHHHHHHHHC-CCcHHHHHH-hHHHHHhcccccCchhHHHHHhcc-CcC-------------------CCCc
Confidence            799999999999998863 334444442 222222    34555555555431 111                   232 


Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC-CchHHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS-LDVFVGSGLID  218 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~  218 (385)
                      ......+...+...|++++|...+++..+.. +.+...+..+...+...|++++|...++........ |+.        
T Consensus       114 ~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~--------  184 (355)
T cd05804         114 WYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSML--------  184 (355)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcch--------
Confidence            3344456678889999999999999998852 334567778888999999999999999998875432 111        


Q ss_pred             HHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCCh--hhHH------HHHHHHHhcCCCCchHHHHHHHH
Q 040338          219 MYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNM--ISWM------VLISAFSQAGVLEKPRFFFFFVS  290 (385)
Q Consensus       219 ~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~--~~~~------~li~~~~~~g~~~~a~~~~~~~~  290 (385)
                                  ....|..+...+...|++++|..++++...++.  ....      .++.-+...|....+.       
T Consensus       185 ------------~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~-------  245 (355)
T cd05804         185 ------------RGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGD-------  245 (355)
T ss_pred             ------------hHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHH-------
Confidence                        112345667778889999999999999764321  2111      1122222233222211       


Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--C---C------cchHHHHHHH
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--P---T------CVIWGALLGA  358 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p---~------~~~~~~li~~  358 (385)
                               .++.+............ .........++...|+.++|..+++.+...  .   .      +...-...-+
T Consensus       246 ---------~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~  316 (355)
T cd05804         246 ---------RWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALY  316 (355)
T ss_pred             ---------HHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHH
Confidence                     11111111111000011 222235677788899999999999887652  1   1      1122223334


Q ss_pred             HHhcCChHHHHHHHHHHHhcc
Q 040338          359 CCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       359 ~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      +...|+.++|.+.+.+.....
T Consensus       317 ~~~~g~~~~A~~~L~~al~~a  337 (355)
T cd05804         317 AFAEGNYATALELLGPVRDDL  337 (355)
T ss_pred             HHHcCCHHHHHHHHHHHHHHH
Confidence            668899999999999887654

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.

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=98.64  E-value=3.6e-05  Score=70.31  Aligned_cols=182  Identities=10%  Similarity=-0.027  Sum_probs=119.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|+-++|......-.+..+ -+.+.|..+.-.+....+.++|++.|......+                   +.|...|-
T Consensus        54 lg~~~ea~~~vr~glr~d~-~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~-------------------~dN~qilr  113 (700)
T KOG1156|consen   54 LGKKEEAYELVRLGLRNDL-KSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE-------------------KDNLQILR  113 (700)
T ss_pred             ccchHHHHHHHHHHhccCc-ccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC-------------------CCcHHHHH
Confidence            6777888777666655432 255566666666666677888888887766554                   46777777


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCC-CCchHHHHHHHHH---
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEP-SLDVFVGSGLIDM---  219 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~---  219 (385)
                      -|--.-.+.++++........+.+.  .|+ ...|..+..+..-.|+...|..++++..+... .|+...|......   
T Consensus       114 DlslLQ~QmRd~~~~~~tr~~LLql--~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~  191 (700)
T KOG1156|consen  114 DLSLLQIQMRDYEGYLETRNQLLQL--RPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQ  191 (700)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHh--hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHH
Confidence            7666667788888888877777764  454 44566777788888999999999999988753 5666665544332   


Q ss_pred             ---HHhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHH
Q 040338          220 ---YLKCGCNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMV  268 (385)
Q Consensus       220 ---~~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~  268 (385)
                         ..+.|..+            +.-....-..-...+.+.+++++|..++..+..  ||..-|+.
T Consensus       192 n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy~  257 (700)
T KOG1156|consen  192 NQILIEAGSLQKALEHLLDNEKQIVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERNPDNLDYYE  257 (700)
T ss_pred             HHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhCchhHHHHH
Confidence               23334322            111222223445666777888888888888876  44444443

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

Probab=98.62  E-value=5.4e-06  Score=66.14  Aligned_cols=181  Identities=11%  Similarity=-0.003  Sum_probs=133.0

Q ss_pred             HHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHh
Q 040338          178 YATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFEL  257 (385)
Q Consensus       178 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  257 (385)
                      ..-|.-.|...|+...|.+-+++.+++.+                       .+..+|..+...|.+.|..+.|.+.|++
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~DP-----------------------s~~~a~~~~A~~Yq~~Ge~~~A~e~Yrk   94 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEHDP-----------------------SYYLAHLVRAHYYQKLGENDLADESYRK   94 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCc-----------------------ccHHHHHHHHHHHHHcCChhhHHHHHHH
Confidence            33455567777777777777777766542                       1223445555566666677777777776


Q ss_pred             ccc---CChhhHHHHHHHHHhcCCCCchHHHH--------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hh
Q 040338          258 MSR---RNMISWMVLISAFSQAGVLEKPRFFF--------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TC  318 (385)
Q Consensus       258 m~~---~~~~~~~~li~~~~~~g~~~~a~~~~--------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~  318 (385)
                      ..+   .+....|....-+|..|++++|...|              +|.++.-+..+.|+.+.|...|++..+..+  +.
T Consensus        95 Alsl~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~  174 (250)
T COG3063          95 ALSLAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPP  174 (250)
T ss_pred             HHhcCCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCCh
Confidence            654   24456666666677777777777777              788888888888899999999999988888  88


Q ss_pred             hHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          319 YFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       319 ~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ....+.....+.|++-.|...++.....  ++..+.-..|+.-.+.|+.+.+-+.=..+.+.-|.
T Consensus       175 ~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~  239 (250)
T COG3063         175 ALLELARLHYKAGDYAPARLYLERYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPY  239 (250)
T ss_pred             HHHHHHHHHHhcccchHHHHHHHHHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            8888899999999999999999988775  66667777777788889988888776666665543

>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=98.61  E-value=1e-06  Score=75.80  Aligned_cols=132  Identities=13%  Similarity=0.023  Sum_probs=86.7

Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhcccC-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSRR-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTA  310 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~  310 (385)
                      .......+..|.+.++++.|.+.++.|.+- +..+..-+..++..                  ...-...+.+|..+|++
T Consensus       131 lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~------------------l~~g~e~~~~A~y~f~E  192 (290)
T PF04733_consen  131 LELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVN------------------LATGGEKYQDAFYIFEE  192 (290)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHH------------------HHHTTTCCCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHH------------------HHhCchhHHHHHHHHHH
Confidence            344445566666666666666666666652 11222223333221                  11112357888999999


Q ss_pred             HHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCCh-HHHHHHHHHHHhcccc
Q 040338          311 MAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNT-KLAELVMRNLLQLDVK  381 (385)
Q Consensus       311 ~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~-~~a~~~~~~~~~~~~~  381 (385)
                      +.....  +.+.+.+..+....|++++|.+++++...+  .+..+...++.+....|+. +.+.+.+.++.+..|.
T Consensus       193 l~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~~p~  268 (290)
T PF04733_consen  193 LSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQSNPN  268 (290)
T ss_dssp             HHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHHTTT
T ss_pred             HHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHhCCC
Confidence            988754  778888999999999999999999998764  3455666777777777877 6788899988877664

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.61  E-value=1.4e-05  Score=66.26  Aligned_cols=300  Identities=14%  Similarity=0.044  Sum_probs=187.8

Q ss_pred             hhhhHHHHHhhhCCCCh---hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhH-HHHHHhcCChhHHHH
Q 040338           33 LIDDDYRVFCDIGPRYL---FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSS-IDMHVKCGAVDYAES  108 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~---~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l-i~~~~~~g~~~~a~~  108 (385)
                      ++++|.+++..-.++++   ...+.+-.+|-.   ..++..|-..++++...  .|...-|... ...+-+.+.+.+|++
T Consensus        25 ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~---~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSLY~A~i~ADALr   99 (459)
T KOG4340|consen   25 RYADAIQLLGSELERSPRSRAGLSLLGYCYYR---LQEFALAAECYEQLGQL--HPELEQYRLYQAQSLYKACIYADALR   99 (459)
T ss_pred             hHHHHHHHHHHHHhcCccchHHHHHHHHHHHH---HHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHHHHhcccHHHHH
Confidence            89999998876554333   334444333333   68899999999999875  4555555432 355667889999999


Q ss_pred             HHHhccCCC-cc-----------ccccchHHHHHHhcCCC-CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC-CCCCC
Q 040338          109 AFLRMLNPS-LF-----------CWKFGIIRLLIMFQKMP-ERDLVSWNTMISILTRHGFGFETLCTFIELWNH-GFGLS  174 (385)
Q Consensus       109 ~~~~m~~~~-~~-----------~~~~~~~~a~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~  174 (385)
                      +...|.... ..           ...+++..+..+.++.+ +.+..+-+...-...+.|+++.|++-|+...+- |..| 
T Consensus       100 V~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqp-  178 (459)
T KOG4340|consen  100 VAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQP-  178 (459)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCc-
Confidence            999887642 21           11177777777888877 355666666666667899999999999998775 4554 


Q ss_pred             HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHH----HHHHHHHHhcCCCC---CCchhhHHHHHHHHHHcCCC
Q 040338          175 SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVG----SGLIDMYLKCGCNG---IESSIQIGKALVTMYAEGGS  247 (385)
Q Consensus       175 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----~~li~~~~~~g~~~---~~~~~~~~~~li~~~~~~g~  247 (385)
                      ...|+..+ ++.+.|+.+.|.+...+++.+|++-.+..-    +..++. ...|+.-   ...-+..+|.-...+.+.|+
T Consensus       179 llAYniAL-aHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDv-rsvgNt~~lh~Sal~eAfNLKaAIeyq~~n  256 (459)
T KOG4340|consen  179 LLAYNLAL-AHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDV-RSVGNTLVLHQSALVEAFNLKAAIEYQLRN  256 (459)
T ss_pred             hhHHHHHH-HHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCch-hcccchHHHHHHHHHHHhhhhhhhhhhccc
Confidence            56777665 667789999999999999998864221110    000000 0000000   01112334444455677899


Q ss_pred             hhHHHHHHHhcccC-----ChhhHHHHHHHHHhcCCCCch---HHHH---------HHHHHHHHhcccCChhhHHHHHHH
Q 040338          248 TQKADLAFELMSRR-----NMISWMVLISAFSQAGVLEKP---RFFF---------FFVSLLSGCSHSGPVTKGKHYFTA  310 (385)
Q Consensus       248 ~~~A~~~~~~m~~~-----~~~~~~~li~~~~~~g~~~~a---~~~~---------~~~~l~~~~~~~~~~~~a~~~~~~  310 (385)
                      .+.|.+-+-.|+-+     |++|...+.-.=.. +++.+.   ++++         ||..++-.||++.-++.|-.++.+
T Consensus       257 ~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~~-~~p~~g~~KLqFLL~~nPfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  257 YEAAQEALTDMPPRAEEELDPVTLHNQALMNMD-ARPTEGFEKLQFLLQQNPFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             HHHHHHHhhcCCCcccccCCchhhhHHHHhccc-CCccccHHHHHHHHhcCCCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            99999999999742     66666554433222 222222   2222         999999999999999988888876


Q ss_pred             HHhccc---hhhHHHHHHHHHc-cCCHHHHHHHHH
Q 040338          311 MAKFTY---TCYFVCMVDLLGL-SGLLGEAKKLID  341 (385)
Q Consensus       311 ~~~~~~---~~~~~~li~~~~~-~g~~~~A~~~~~  341 (385)
                      -...-.   ....--|++++.. .-..++|.+-++
T Consensus       336 n~~lTyk~L~~Yly~LLdaLIt~qT~pEea~KKL~  370 (459)
T KOG4340|consen  336 NAHLTYKFLTPYLYDLLDALITCQTAPEEAFKKLD  370 (459)
T ss_pred             CcchhHHHhhHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            544333   2222234444443 334555555443

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

Probab=98.60  E-value=1.5e-05  Score=71.67  Aligned_cols=183  Identities=11%  Similarity=0.073  Sum_probs=127.1

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      ..|-.....|+-.|..+.|+..|...-+. ++-..-.+-.+---|.+.+..+.|.++|.+.....+              
T Consensus       347 paWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai~P--------------  411 (611)
T KOG1173|consen  347 PAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAEKFFKQALAIAP--------------  411 (611)
T ss_pred             HHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHHHHHHHHHhcCC--------------
Confidence            46888888888899999999888877653 222233344455567888899999999988876532              


Q ss_pred             HhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH--HHHHHHHHhccc
Q 040338          221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF--FFVSLLSGCSHS  298 (385)
Q Consensus       221 ~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~--~~~~l~~~~~~~  298 (385)
                               .|....+-+.-.....+.+.+|...|.....+        |..-.     .+-. .|  +++.+..+|.+.
T Consensus       412 ---------~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~--------ik~~~-----~e~~-~w~p~~~NLGH~~Rkl  468 (611)
T KOG1173|consen  412 ---------SDPLVLHELGVVAYTYEEYPEALKYFQKALEV--------IKSVL-----NEKI-FWEPTLNNLGHAYRKL  468 (611)
T ss_pred             ---------CcchhhhhhhheeehHhhhHHHHHHHHHHHHH--------hhhcc-----cccc-chhHHHHhHHHHHHHH
Confidence                     23334455555566677899999999876521        11000     1111 22  667777777778


Q ss_pred             CChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCCcchHHHHHHHHHh
Q 040338          299 GPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPTCVIWGALLGACCS  361 (385)
Q Consensus       299 ~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~~~~~~~li~~~~~  361 (385)
                      +..++|+..+++.....+  ..++.++.-.|...|+++.|...|++..- +|+-.+-+.++..+..
T Consensus       469 ~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  469 NKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLAIE  534 (611)
T ss_pred             hhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHHHH
Confidence            888888888888777777  88888888888889999999998888766 3776666666654433

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.58  E-value=4e-05  Score=65.10  Aligned_cols=94  Identities=11%  Similarity=0.015  Sum_probs=72.2

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcch-HHHHHHHHHhcCCh
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVI-WGALLGACCSHYNT  365 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~-~~~li~~~~~~g~~  365 (385)
                      .+..+++..|+..+|+++|-.+.....   ......|.++|.++++++.|+.++-.+....+..+ ...+.+-|.+.+++
T Consensus       398 N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eF  477 (557)
T KOG3785|consen  398 NLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKTNTPSERFSLLQLIANDCYKANEF  477 (557)
T ss_pred             HHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence            466677778899999999988766554   33345677889999999999999988876433333 44455788999999


Q ss_pred             HHHHHHHHHHHhccccCC
Q 040338          366 KLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~~  383 (385)
                      --|-+.|+++...+|.|.
T Consensus       478 yyaaKAFd~lE~lDP~pE  495 (557)
T KOG3785|consen  478 YYAAKAFDELEILDPTPE  495 (557)
T ss_pred             HHHHHhhhHHHccCCCcc
Confidence            999999999998888874

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

Probab=98.52  E-value=0.00041  Score=66.90  Aligned_cols=113  Identities=14%  Similarity=0.086  Sum_probs=86.5

Q ss_pred             ChhhHHHHHHHHHhcCCCCchHHHH-------HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCH
Q 040338          262 NMISWMVLISAFSQAGVLEKPRFFF-------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLL  333 (385)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~a~~~~-------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~  333 (385)
                      ....|+.+..+-.+.|...+|++-|       .|..++..+.+.|.+++..+.+....+... +.+-+.||-+|++.+++
T Consensus      1103 ~p~vWsqlakAQL~~~~v~dAieSyikadDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~eLi~AyAkt~rl 1182 (1666)
T KOG0985|consen 1103 EPAVWSQLAKAQLQGGLVKDAIESYIKADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDSELIFAYAKTNRL 1182 (1666)
T ss_pred             ChHHHHHHHHHHHhcCchHHHHHHHHhcCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchHHHHHHHHHhchH
Confidence            3467888888888999999999888       899999999999999999999998888877 88888899999999999


Q ss_pred             HHHHHHHHhCCC-------------------C---CCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          334 GEAKKLIDEMPS-------------------K---PTCVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       334 ~~A~~~~~~m~~-------------------~---p~~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      .+.++++..-..                   +   .++..|..|...++..|+++.|....++
T Consensus      1183 ~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRK 1245 (1666)
T KOG0985|consen 1183 TELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARK 1245 (1666)
T ss_pred             HHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhh
Confidence            998877532110                   0   2344455566666666666666554444

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.52  E-value=0.00014  Score=67.84  Aligned_cols=236  Identities=12%  Similarity=0.023  Sum_probs=153.1

Q ss_pred             HHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC-------------------C
Q 040338          148 SILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS-------------------L  208 (385)
Q Consensus       148 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-------------------~  208 (385)
                      --|+..++.+.|.+..++..+.+-.-+...+..+.-.+...+++.+|+.+.+.....-..                   .
T Consensus       486 lq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~~~~~~e~  565 (799)
T KOG4162|consen  486 LQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIELTFNDREE  565 (799)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhhhcccHHH
Confidence            345667889999999999888765667778888888888888999999888876653111                   1


Q ss_pred             chHHHHHHHHHHHh---------cC------------CCCCCchhhHHHHHHHHHH---cCCChhHHHHHHHhcccCCh-
Q 040338          209 DVFVGSGLIDMYLK---------CG------------CNGIESSIQIGKALVTMYA---EGGSTQKADLAFELMSRRNM-  263 (385)
Q Consensus       209 ~~~~~~~li~~~~~---------~g------------~~~~~~~~~~~~~li~~~~---~~g~~~~A~~~~~~m~~~~~-  263 (385)
                      ...|...++..+-.         .|            ..+..-...++..+..-..   +.-..+..+..+.-...|+. 
T Consensus       566 ~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~  645 (799)
T KOG4162|consen  566 ALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSL  645 (799)
T ss_pred             HHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccccCCCCch
Confidence            12222233332220         00            0001111222222222111   11111222111111112221 


Q ss_pred             -----hhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHH
Q 040338          264 -----ISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMV  324 (385)
Q Consensus       264 -----~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li  324 (385)
                           ..|......+.+.++.++|...+            .|......+...|.+++|.+.|......++  +....++.
T Consensus       646 ~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~hv~s~~Ala  725 (799)
T KOG4162|consen  646 WYLLQKLWLLAADLFLLSGNDDEARSCLLEASKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPDHVPSMTALA  725 (799)
T ss_pred             HHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHHH
Confidence                 23444556677778888776444            455555566678899999999999888888  88999999


Q ss_pred             HHHHccCCHHHHHH--HHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          325 DLLGLSGLLGEAKK--LIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       325 ~~~~~~g~~~~A~~--~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .++.+.|+..-|.+  ++.++.+-  .+...|-.+...+.+.|+.+.|-+.|+...++....|
T Consensus       726 ~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qLe~S~P  788 (799)
T KOG4162|consen  726 ELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQLEESNP  788 (799)
T ss_pred             HHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhhccCCC
Confidence            99999998888888  99988773  4678899999999999999999999999988766544

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.52  E-value=1.6e-05  Score=73.57  Aligned_cols=183  Identities=11%  Similarity=0.007  Sum_probs=106.3

Q ss_pred             HHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCC----CchhhHHHHHHHHHHcCCChhHHHHHHHh
Q 040338          182 FSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGI----ESSIQIGKALVTMYAEGGSTQKADLAFEL  257 (385)
Q Consensus       182 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~----~~~~~~~~~li~~~~~~g~~~~A~~~~~~  257 (385)
                      +.+....++|.+|+.+++.+.+....  ..-|..+.+.|...|++++    -.....++--|.+|.+.|+|+.|.++-++
T Consensus       739 ieaai~akew~kai~ildniqdqk~~--s~yy~~iadhyan~~dfe~ae~lf~e~~~~~dai~my~k~~kw~da~kla~e  816 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQKTA--SGYYGEIADHYANKGDFEIAEELFTEADLFKDAIDMYGKAGKWEDAFKLAEE  816 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhccc--cccchHHHHHhccchhHHHHHHHHHhcchhHHHHHHHhccccHHHHHHHHHH
Confidence            34444455555555555555443221  1223333444444444431    11122356678899999999999999988


Q ss_pred             cccC--ChhhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccC
Q 040338          258 MSRR--NMISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSG  331 (385)
Q Consensus       258 m~~~--~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g  331 (385)
                      ...|  .+..|-+-..-+-.+|++.+|.+++    -=...|..|-+.|..+..+++.++-.-.....+...+..-|-..|
T Consensus       817 ~~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmirlv~k~h~d~l~dt~~~f~~e~e~~g  896 (1636)
T KOG3616|consen  817 CHGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMIRLVEKHHGDHLHDTHKHFAKELEAEG  896 (1636)
T ss_pred             hcCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHHHHHHHhChhhhhHHHHHHHHHHHhcc
Confidence            8776  3456666667788899999998876    112233344444444444444333222222555566677777788


Q ss_pred             CHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHH
Q 040338          332 LLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       332 ~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      ++.+|..-|-+..+      |.+.++.|..++.|++|.++.
T Consensus       897 ~lkaae~~flea~d------~kaavnmyk~s~lw~dayria  931 (1636)
T KOG3616|consen  897 DLKAAEEHFLEAGD------FKAAVNMYKASELWEDAYRIA  931 (1636)
T ss_pred             ChhHHHHHHHhhhh------HHHHHHHhhhhhhHHHHHHHH
Confidence            88888877765543      455666666666666665554

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.49  E-value=2.4e-07  Score=51.93  Aligned_cols=35  Identities=31%  Similarity=0.379  Sum_probs=31.9

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  175 (385)
                      .+||++|.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999973

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.

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

Probab=98.47  E-value=0.00021  Score=68.76  Aligned_cols=229  Identities=10%  Similarity=0.027  Sum_probs=166.0

Q ss_pred             HHHhcCChhHHHHHHHhccCCCcc----ccc-cchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCC
Q 040338           96 MHVKCGAVDYAESAFLRMLNPSLF----CWK-FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHG  170 (385)
Q Consensus        96 ~~~~~g~~~~a~~~~~~m~~~~~~----~~~-~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  170 (385)
                      .....+-.++|..+|+...-....    ..+ +.+++|.++-+++.+|.  +|..+..+-.+.|...+|++-|-+.    
T Consensus      1057 iai~~~LyEEAF~ifkkf~~n~~A~~VLie~i~~ldRA~efAe~~n~p~--vWsqlakAQL~~~~v~dAieSyika---- 1130 (1666)
T KOG0985|consen 1057 IAIENQLYEEAFAIFKKFDMNVSAIQVLIENIGSLDRAYEFAERCNEPA--VWSQLAKAQLQGGLVKDAIESYIKA---- 1130 (1666)
T ss_pred             HHhhhhHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHHHHHHhhCChH--HHHHHHHHHHhcCchHHHHHHHHhc----
Confidence            344455566777777654322211    111 67777777777766654  6999999999999999998877443    


Q ss_pred             CCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------CCchhhHHHHHHHHHHc
Q 040338          171 FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------IESSIQIGKALVTMYAE  244 (385)
Q Consensus       171 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------~~~~~~~~~~li~~~~~  244 (385)
                        -|...|..+++.+.+.|.+++-.+.+....+..-+|...  +.||-+|++.++..      ..|+..-...+.+-|..
T Consensus      1131 --dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~ 1206 (1666)
T KOG0985|consen 1131 --DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFE 1206 (1666)
T ss_pred             --CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhh
Confidence              367789999999999999999999998888877666554  57888999988776      67888888888888888


Q ss_pred             CCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH-------HHHHHHHHhcccCChhhHHHHHHHHHhccc-
Q 040338          245 GGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF-------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-  316 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~-------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-  316 (385)
                      .|.++.|.-+|...     .-|..|...+...|++..|.+.-       +|-.+--+|...+.+..|.     |.-.+. 
T Consensus      1207 ~~~y~aAkl~y~~v-----SN~a~La~TLV~LgeyQ~AVD~aRKAns~ktWK~VcfaCvd~~EFrlAQ-----iCGL~ii 1276 (1666)
T KOG0985|consen 1207 EKMYEAAKLLYSNV-----SNFAKLASTLVYLGEYQGAVDAARKANSTKTWKEVCFACVDKEEFRLAQ-----ICGLNII 1276 (1666)
T ss_pred             hhhhHHHHHHHHHh-----hhHHHHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHhchhhhhHHH-----hcCceEE
Confidence            89998888888544     56778888888888888777666       7777777777766544332     222222 


Q ss_pred             --hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          317 --TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       317 --~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                        ..-..-++..|-..|-+++.+.+++.-.
T Consensus      1277 vhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1277 VHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             EehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence              4555667777777777777777776554

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.46  E-value=0.00062  Score=63.78  Aligned_cols=302  Identities=15%  Similarity=0.034  Sum_probs=181.2

Q ss_pred             ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc---cccc---------cchHHHHHHhcCCCCC-----CcchHH
Q 040338           82 YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL---FCWK---------FGIIRLLIMFQKMPER-----DLVSWN  144 (385)
Q Consensus        82 g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~~~~---------~~~~~a~~~~~~~~~~-----~~~~~~  144 (385)
                      .+.-+..+|..|--++.++|+++.+.+.|++...--.   ..|.         |.-..|..++++..++     |+..+-
T Consensus       318 ~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~L  397 (799)
T KOG4162|consen  318 KFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLL  397 (799)
T ss_pred             hhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHH
Confidence            4556788888888888888888888888887643211   1111         5555566665554322     222222


Q ss_pred             HHHHHHH-hCCCchHHHHHHHHHHHC--CC--CCCHhhHHHHHHHhcCc----c-------CccchhhHHHHHHHhCC-C
Q 040338          145 TMISILT-RHGFGFETLCTFIELWNH--GF--GLSSMLYATAFSARASV----Y-------DLEWGPHLHSRVVHMEP-S  207 (385)
Q Consensus       145 ~li~~~~-~~~~~~~a~~~~~~m~~~--g~--~p~~~t~~~ll~~~~~~----~-------~~~~a~~~~~~~~~~~~-~  207 (385)
                      ..-..|. +.+..++++++-.+....  |.  ......|..+--+|...    .       ...++.+.+++.++.+. .
T Consensus       398 masklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~d  477 (799)
T KOG4162|consen  398 MASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTD  477 (799)
T ss_pred             HHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            2222332 335666666666665541  11  11223333333333322    1       13455666666666544 3


Q ss_pred             CchHHHHHHHHHHHhcC-----------CCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CC------------
Q 040338          208 LDVFVGSGLIDMYLKCG-----------CNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RN------------  262 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g-----------~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~------------  262 (385)
                      |+...|-++=.+..+.=           ......+...|..+...+...+++.+|+.+.+....  ++            
T Consensus       478 p~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~  557 (799)
T KOG4162|consen  478 PLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIE  557 (799)
T ss_pred             chHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhh
Confidence            44444433322221110           111456677888888888888888888888775543  11            


Q ss_pred             ---------hhhHHHHHHHHH------hcC-----------------CCCchHHHH------------------------
Q 040338          263 ---------MISWMVLISAFS------QAG-----------------VLEKPRFFF------------------------  286 (385)
Q Consensus       263 ---------~~~~~~li~~~~------~~g-----------------~~~~a~~~~------------------------  286 (385)
                               ..|...++...-      ..+                 +..++....                        
T Consensus       558 ~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~  637 (799)
T KOG4162|consen  558 LTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSST  637 (799)
T ss_pred             hhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCccc
Confidence                     112222211111      000                 111111111                        


Q ss_pred             --------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCC-
Q 040338          287 --------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPT-  348 (385)
Q Consensus       287 --------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~-  348 (385)
                                    .|......+.+.+..+++...+.+..+..+  ...|......+...|...+|.+.|..... .|+ 
T Consensus       638 ~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~h  717 (799)
T KOG4162|consen  638 VLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPDH  717 (799)
T ss_pred             ccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCCC
Confidence                          566777778888888999888888888777  77777788888999999999999988766 354 


Q ss_pred             cchHHHHHHHHHhcCChHHHHH--HHHHHHhccccCC
Q 040338          349 CVIWGALLGACCSHYNTKLAEL--VMRNLLQLDVKVF  383 (385)
Q Consensus       349 ~~~~~~li~~~~~~g~~~~a~~--~~~~~~~~~~~~~  383 (385)
                      +.+-+++...+.+.|+...|..  ++.++.+.+|.+.
T Consensus       718 v~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~  754 (799)
T KOG4162|consen  718 VPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNH  754 (799)
T ss_pred             cHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCH
Confidence            5578889999999999888888  9999999998765

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.46  E-value=5e-05  Score=71.35  Aligned_cols=303  Identities=13%  Similarity=-0.004  Sum_probs=174.9

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh-cc--------CCCchHHHhHHHHHHhcCCh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF-YF--------VSDESIAKSSIDMHVKCGAV  103 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-g~--------~~~~~~~~~li~~~~~~g~~  103 (385)
                      +.+.|.+-.+.+.  +-..|..|.+.+.+   .++++.|.-.+..|... |.        .|+ ++=..+.-.-.+.|.+
T Consensus       743 ~MD~AfksI~~Ik--S~~vW~nmA~McVk---T~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMl  816 (1416)
T KOG3617|consen  743 SMDAAFKSIQFIK--SDSVWDNMASMCVK---TRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGML  816 (1416)
T ss_pred             cHHHHHHHHHHHh--hhHHHHHHHHHhhh---hccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhH
Confidence            8888888777655  45578888888444   78888888777777642 21        222 2222333344567899


Q ss_pred             hHHHHHHHhccCCCccccc----cchHHHHHHhcCCCCC-CcchHHHHHHHHHhCCCchHHHHHHHHHHH----------
Q 040338          104 DYAESAFLRMLNPSLFCWK----FGIIRLLIMFQKMPER-DLVSWNTMISILTRHGFGFETLCTFIELWN----------  168 (385)
Q Consensus       104 ~~a~~~~~~m~~~~~~~~~----~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------  168 (385)
                      ++|+.+|.+-+..+....-    |.+++|.++-+.-..- =..||......+-..++.+.|++.|++-..          
T Consensus       817 EeA~~lYr~ckR~DLlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~  896 (1416)
T KOG3617|consen  817 EEALILYRQCKRYDLLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLK  896 (1416)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHH
Confidence            9999999887766543222    6666666665443211 123555555555556667777666655211          


Q ss_pred             CC---------CCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHH
Q 040338          169 HG---------FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALV  239 (385)
Q Consensus       169 ~g---------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li  239 (385)
                      ..         -..|...|...-..+-..|+.+.|+.+|+...+                               |-+++
T Consensus       897 e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D-------------------------------~fs~V  945 (1416)
T KOG3617|consen  897 EYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD-------------------------------YFSMV  945 (1416)
T ss_pred             hChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh-------------------------------hhhhe
Confidence            00         011223333333333444555555555444432                               34555


Q ss_pred             HHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHHhcc
Q 040338          240 TMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMAKFT  315 (385)
Q Consensus       240 ~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  315 (385)
                      +..+-.|+.++|-.+-++-  .|......|...|-..|+..+|+.+|    +|.+.|..|..++.-++...+--......
T Consensus       946 rI~C~qGk~~kAa~iA~es--gd~AAcYhlaR~YEn~g~v~~Av~FfTrAqafsnAIRlcKEnd~~d~L~nlal~s~~~d 1023 (1416)
T KOG3617|consen  946 RIKCIQGKTDKAARIAEES--GDKAACYHLARMYENDGDVVKAVKFFTRAQAFSNAIRLCKENDMKDRLANLALMSGGSD 1023 (1416)
T ss_pred             eeEeeccCchHHHHHHHhc--ccHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhhcCchh
Confidence            5666667777776665543  35667777888899999999999988    78888888777665544332221111111


Q ss_pred             c----------hhhHHHHHHHHHccCCHHHHHHHHHhCCC-------------CCCcchHHHHHHHHHhcCChHHHHHHH
Q 040338          316 Y----------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-------------KPTCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       316 ~----------~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------------~p~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      .          ......-+..|-++|.+..|+++-=+-.+             ..|+...+.-...++...++++|..++
T Consensus      1024 ~v~aArYyEe~g~~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL 1103 (1416)
T KOG3617|consen 1024 LVSAARYYEELGGYAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLL 1103 (1416)
T ss_pred             HHHHHHHHHHcchhhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            1          22233445677888888888776432222             134445555555566666666666655


Q ss_pred             HH
Q 040338          373 RN  374 (385)
Q Consensus       373 ~~  374 (385)
                      -.
T Consensus      1104 ~~ 1105 (1416)
T KOG3617|consen 1104 CL 1105 (1416)
T ss_pred             HH
Confidence            43

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.44  E-value=3.8e-07  Score=50.75  Aligned_cols=33  Identities=18%  Similarity=0.224  Sum_probs=30.1

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGL  173 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  173 (385)
                      .+||++|.+|++.|+++.|.++|++|.+.|++|
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            589999999999999999999999999999887

>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=98.43  E-value=1e-06  Score=75.75  Aligned_cols=208  Identities=10%  Similarity=-0.033  Sum_probs=130.4

Q ss_pred             HHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC
Q 040338          148 SILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG  227 (385)
Q Consensus       148 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  227 (385)
                      +-+.-.|++..++.-.+ .....-..+......+.+++...|+.+.+   +.++.... .|.....              
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~v---l~ei~~~~-~~~l~av--------------   69 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSV---LSEIKKSS-SPELQAV--------------   69 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHH---HHHS-TTS-SCCCHHH--------------
T ss_pred             HHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHH---HHHhccCC-ChhHHHH--------------
Confidence            44555788888886555 22221122344556678888888876533   33433332 3444333              


Q ss_pred             CCchhhHHHHHHHHHHcCCChhHHHHHHHhcc-cC---ChhhHHH-HHHHHHhcCCCCchHHHH-------HHHHHHHHh
Q 040338          228 IESSIQIGKALVTMYAEGGSTQKADLAFELMS-RR---NMISWMV-LISAFSQAGVLEKPRFFF-------FFVSLLSGC  295 (385)
Q Consensus       228 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~---~~~~~~~-li~~~~~~g~~~~a~~~~-------~~~~l~~~~  295 (385)
                              ..+...+...++-+.+..-+++.. ++   +..++.. ....+...|++++|++++       .....+..+
T Consensus        70 --------~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~~~lE~~al~Vqi~  141 (290)
T PF04733_consen   70 --------RLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKGGSLELLALAVQIL  141 (290)
T ss_dssp             --------HHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTTTCHHHHHHHHHHH
T ss_pred             --------HHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHccCcccHHHHHHHHH
Confidence                    222222222234455555554433 22   1122222 234456678888888777       667788899


Q ss_pred             cccCChhhHHHHHHHHHhccc----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      .+.++++.|.+.++.|.+.+.    .....+.+....-.+++.+|..+|+++.++  ++..+.+.+..++...|++++|.
T Consensus       142 L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe  221 (290)
T PF04733_consen  142 LKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAE  221 (290)
T ss_dssp             HHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHH
Confidence            999999999999999998777    333344444444456799999999999886  67788899999999999999999


Q ss_pred             HHHHHHHhccccC
Q 040338          370 LVMRNLLQLDVKV  382 (385)
Q Consensus       370 ~~~~~~~~~~~~~  382 (385)
                      +++++..+.++.+
T Consensus       222 ~~L~~al~~~~~~  234 (290)
T PF04733_consen  222 ELLEEALEKDPND  234 (290)
T ss_dssp             HHHHHHCCC-CCH
T ss_pred             HHHHHHHHhccCC
Confidence            9999998877764

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.

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

Probab=98.42  E-value=0.00012  Score=58.72  Aligned_cols=164  Identities=14%  Similarity=0.040  Sum_probs=127.1

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHH
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIM  131 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~  131 (385)
                      .-.+--+|..   .|+...|.+-+++.++.. +.+..+|..+...|-+.|..+.|.+-|++..+..              
T Consensus        38 rlqLal~YL~---~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~--------------   99 (250)
T COG3063          38 RLQLALGYLQ---QGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLA--------------   99 (250)
T ss_pred             HHHHHHHHHH---CCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC--------------
Confidence            3444455555   899999999999999874 3356788888899999999999999998887665              


Q ss_pred             hcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCch
Q 040338          132 FQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDV  210 (385)
Q Consensus       132 ~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  210 (385)
                           +.+-.+.|..-..+|..|++++|...|++....-.-| -..||..+.-+..+.|+.+.|...+++.++....-+ 
T Consensus       100 -----p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~-  173 (250)
T COG3063         100 -----PNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFP-  173 (250)
T ss_pred             -----CCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCC-
Confidence                 4667788888888899999999999999988753222 356788888888899999999999999888754322 


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC
Q 040338          211 FVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR  261 (385)
Q Consensus       211 ~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  261 (385)
                                            .+.-.+.+...+.|++..|...++.....
T Consensus       174 ----------------------~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~  202 (250)
T COG3063         174 ----------------------PALLELARLHYKAGDYAPARLYLERYQQR  202 (250)
T ss_pred             ----------------------hHHHHHHHHHHhcccchHHHHHHHHHHhc
Confidence                                  22355666777788888888888777653

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.42  E-value=0.00026  Score=60.11  Aligned_cols=309  Identities=11%  Similarity=0.009  Sum_probs=204.3

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHH-hHHHHHHhcCChhHHHHHHH
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAK-SSIDMHVKCGAVDYAESAFL  111 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~-~li~~~~~~g~~~~a~~~~~  111 (385)
                      .+.+|+.-|+.....|+..|-++.+-...+...|+-.-|+.=+....+.  +||-..-. .-...+.+.|.++.|..=|+
T Consensus        53 Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQRg~vllK~Gele~A~~DF~  130 (504)
T KOG0624|consen   53 QLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQRGVVLLKQGELEQAEADFD  130 (504)
T ss_pred             hHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHhchhhhhcccHHHHHHHHH
Confidence            6777888888777778888888777655555578888888888888774  56643322 12356778899999999998


Q ss_pred             hccCCCccccccchHHHHHHhcCCCCCCcchHH--HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc
Q 040338          112 RMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN--TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY  189 (385)
Q Consensus       112 ~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~  189 (385)
                      .+.+.+.-  +|...++.+-+    .+....|+  ..+..+.-.|+...|+.....+.+. .+-|...|..-..+|...|
T Consensus       131 ~vl~~~~s--~~~~~eaqskl----~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi-~~Wda~l~~~Rakc~i~~~  203 (504)
T KOG0624|consen  131 QVLQHEPS--NGLVLEAQSKL----ALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEI-QPWDASLRQARAKCYIAEG  203 (504)
T ss_pred             HHHhcCCC--cchhHHHHHHH----HhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhc-CcchhHHHHHHHHHHHhcC
Confidence            88766530  01111111110    01111222  2334556678888888888888874 2337777777788888888


Q ss_pred             CccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHH
Q 040338          190 DLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWM  267 (385)
Q Consensus       190 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~  267 (385)
                      ++..|+.=+....+..                       ..++.+.--+-..+...|+.+.++....+..+  ||-..+-
T Consensus       204 e~k~AI~Dlk~askLs-----------------------~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKldpdHK~Cf  260 (504)
T KOG0624|consen  204 EPKKAIHDLKQASKLS-----------------------QDNTEGHYKISQLLYTVGDAENSLKEIRECLKLDPDHKLCF  260 (504)
T ss_pred             cHHHHHHHHHHHHhcc-----------------------ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccCcchhhHH
Confidence            8888876666554432                       12445556777788888998888888887765  4432211


Q ss_pred             HHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHHH
Q 040338          268 VLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLID  341 (385)
Q Consensus       268 ~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~  341 (385)
                      ..-.-+   .+..+.     . .-+....+.++|.++..-.+...+..+      ...+..+-.++...|++.+|++...
T Consensus       261 ~~YKkl---kKv~K~-----l-es~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~  331 (504)
T KOG0624|consen  261 PFYKKL---KKVVKS-----L-ESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCK  331 (504)
T ss_pred             HHHHHH---HHHHHH-----H-HHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHH
Confidence            111100   000000     0 012233566778888888888777666      4455667778888999999999998


Q ss_pred             hCCCC-CC-cchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          342 EMPSK-PT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       342 ~m~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +..+- |+ +.++.-=..+|.-..+++.|+.-|+...+.++.+
T Consensus       332 evL~~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n~sn  374 (504)
T KOG0624|consen  332 EVLDIDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALELNESN  374 (504)
T ss_pred             HHHhcCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCccc
Confidence            88774 44 7788888889999999999999999998887765

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

Probab=98.38  E-value=0.00019  Score=64.58  Aligned_cols=150  Identities=12%  Similarity=-0.099  Sum_probs=86.6

Q ss_pred             hhhhHHHHHhhhC--CC-ChhhHHHHHHHHHh-hhccCChHHHHHHHHHHHHhccCCC-chHHHhHHHHHHhcCChhHHH
Q 040338           33 LIDDDYRVFCDIG--PR-YLFTYNTMINGGVR-CLCVGNIKMALHLHGLVKKFYFVSD-ESIAKSSIDMHVKCGAVDYAE  107 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~-~~~~~~~li~~~~~-~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~a~  107 (385)
                      ++++|..++++..  .| |...+.. ...+.. ....+....+.+.+..  ..+..|+ ......+...+...|++++|.
T Consensus        58 ~~~~A~~~~~~~l~~~P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~~~~A~  134 (355)
T cd05804          58 DLPKALALLEQLLDDYPRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQYDRAE  134 (355)
T ss_pred             CHHHHHHHHHHHHHHCCCcHHHHHH-hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCCHHHHH
Confidence            7777777777654  23 2323331 111111 1113555555555544  1112222 233344556777788888888


Q ss_pred             HHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCC-CCCH--hhHHHHHHH
Q 040338          108 SAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGF-GLSS--MLYATAFSA  184 (385)
Q Consensus       108 ~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~~--~t~~~ll~~  184 (385)
                      +.+++..+.+                   +.+...+..+...+...|++++|...+++..+... .|+.  ..|..+...
T Consensus       135 ~~~~~al~~~-------------------p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~  195 (355)
T cd05804         135 EAARRALELN-------------------PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALF  195 (355)
T ss_pred             HHHHHHHhhC-------------------CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHH
Confidence            8887776655                   34556677777777778888888888777765421 1222  234456667


Q ss_pred             hcCccCccchhhHHHHHHHh
Q 040338          185 RASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       185 ~~~~~~~~~a~~~~~~~~~~  204 (385)
                      +...|++++|..+++.....
T Consensus       196 ~~~~G~~~~A~~~~~~~~~~  215 (355)
T cd05804         196 YLERGDYEAALAIYDTHIAP  215 (355)
T ss_pred             HHHCCCHHHHHHHHHHHhcc
Confidence            77778888888888776543

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.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.38  E-value=1.3e-05  Score=67.50  Aligned_cols=150  Identities=11%  Similarity=-0.059  Sum_probs=107.1

Q ss_pred             hhhHHHHHHHHHHcCCChhHHHHHHHhccc--CCh----hhHHHHHHHHHhcCCCCchHHHH---------------HHH
Q 040338          231 SIQIGKALVTMYAEGGSTQKADLAFELMSR--RNM----ISWMVLISAFSQAGVLEKPRFFF---------------FFV  289 (385)
Q Consensus       231 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~----~~~~~li~~~~~~g~~~~a~~~~---------------~~~  289 (385)
                      ....+-.+...+.+.|++++|...|+++.+  |+.    ..+..+..++...|++++|+..+               ++.
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~  111 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYY  111 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHH
Confidence            344455666677777788888888877764  321    35566677777788888887777               233


Q ss_pred             HHHHHhcc--------cCChhhHHHHHHHHHhccc--hhhH-----------------HHHHHHHHccCCHHHHHHHHHh
Q 040338          290 SLLSGCSH--------SGPVTKGKHYFTAMAKFTY--TCYF-----------------VCMVDLLGLSGLLGEAKKLIDE  342 (385)
Q Consensus       290 ~l~~~~~~--------~~~~~~a~~~~~~~~~~~~--~~~~-----------------~~li~~~~~~g~~~~A~~~~~~  342 (385)
                      .+..++..        .|+.+.|.+.++.+.+..+  ....                 ..+...|.+.|++++|...+++
T Consensus       112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~  191 (235)
T TIGR03302       112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFET  191 (235)
T ss_pred             HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            33333333        2778889999998887666  1111                 1345678889999999999999


Q ss_pred             CCCC-CC----cchHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          343 MPSK-PT----CVIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       343 m~~~-p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      ..+. |+    ...+..+..++.+.|++++|...++.+....+
T Consensus       192 al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~  234 (235)
T TIGR03302       192 VVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYP  234 (235)
T ss_pred             HHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            8764 43    35788999999999999999999999887654

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).

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.31  E-value=2.1e-05  Score=72.86  Aligned_cols=203  Identities=13%  Similarity=0.018  Sum_probs=154.4

Q ss_pred             CCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHH
Q 040338           85 SDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFI  164 (385)
Q Consensus        85 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~  164 (385)
                      |--..-..+...+.+.|-...|..+|++.                           ..|.-+|.+|+..|+..+|..+..
T Consensus       396 p~Wq~q~~laell~slGitksAl~I~Erl---------------------------emw~~vi~CY~~lg~~~kaeei~~  448 (777)
T KOG1128|consen  396 PIWQLQRLLAELLLSLGITKSALVIFERL---------------------------EMWDPVILCYLLLGQHGKAEEINR  448 (777)
T ss_pred             CcchHHHHHHHHHHHcchHHHHHHHHHhH---------------------------HHHHHHHHHHHHhcccchHHHHHH
Confidence            33344456778888899999999999764                           468888999999999999999998


Q ss_pred             HHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc
Q 040338          165 ELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE  244 (385)
Q Consensus       165 ~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~  244 (385)
                      .-.+  -+||...|..+.+......-+++|.++.+.....-                             -..+.....+
T Consensus       449 q~le--k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA-----------------------------~r~~~~~~~~  497 (777)
T KOG1128|consen  449 QELE--KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARA-----------------------------QRSLALLILS  497 (777)
T ss_pred             HHhc--CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHH-----------------------------HHhhcccccc
Confidence            8877  47899999888888777777788887777654320                             0111112233


Q ss_pred             CCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHH
Q 040338          245 GGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFT  309 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~  309 (385)
                      .++++++.+.|+.-.+-   -..+|-....+..+.++...|.+.|            .||++-.+|.+.++-.+|...++
T Consensus       498 ~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~  577 (777)
T KOG1128|consen  498 NKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLK  577 (777)
T ss_pred             chhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHH
Confidence            56888888888755442   3467777777777888888888877            88999999999999999999999


Q ss_pred             HHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          310 AMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       310 ~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      +..+.+.  ..++...+-.....|.+++|.+.+.++..
T Consensus       578 EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  578 EALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             HHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence            9888776  66677777778889999999998887765

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.30  E-value=0.00014  Score=68.41  Aligned_cols=306  Identities=11%  Similarity=0.002  Sum_probs=146.6

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLR  112 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  112 (385)
                      =+++|..++.+-.+-|.  .|.+..+      .|++++|.++-+.=.+-.+   ..||..-...+-..++.+.|++.|++
T Consensus       815 MlEeA~~lYr~ckR~DL--lNKlyQs------~g~w~eA~eiAE~~DRiHL---r~Tyy~yA~~Lear~Di~~AleyyEK  883 (1416)
T KOG3617|consen  815 MLEEALILYRQCKRYDL--LNKLYQS------QGMWSEAFEIAETKDRIHL---RNTYYNYAKYLEARRDIEAALEYYEK  883 (1416)
T ss_pred             hHHHHHHHHHHHHHHHH--HHHHHHh------cccHHHHHHHHhhccceeh---hhhHHHHHHHHHhhccHHHHHHHHHh
Confidence            55666666665544332  2333333      6777777666544333222   23455555555556777777777765


Q ss_pred             ccCCCccccc---cchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC----------C---------
Q 040338          113 MLNPSLFCWK---FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH----------G---------  170 (385)
Q Consensus       113 m~~~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----------g---------  170 (385)
                      -..+-.....   .++.....+..++..  ...|.-....+-..|+.+.|+.+|...++.          |         
T Consensus       884 ~~~hafev~rmL~e~p~~~e~Yv~~~~d--~~L~~WWgqYlES~GemdaAl~~Y~~A~D~fs~VrI~C~qGk~~kAa~iA  961 (1416)
T KOG3617|consen  884 AGVHAFEVFRMLKEYPKQIEQYVRRKRD--ESLYSWWGQYLESVGEMDAALSFYSSAKDYFSMVRIKCIQGKTDKAARIA  961 (1416)
T ss_pred             cCChHHHHHHHHHhChHHHHHHHHhccc--hHHHHHHHHHHhcccchHHHHHHHHHhhhhhhheeeEeeccCchHHHHHH
Confidence            4322110000   222222223333322  333444444455567777777777765432          0         


Q ss_pred             -CCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC---------CCch---------
Q 040338          171 -FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG---------IESS---------  231 (385)
Q Consensus       171 -~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~---------~~~~---------  231 (385)
                       -.-|......+.+-|-..|++.+|..+|-+..         +++..|+.+-..+-.+         -..|         
T Consensus       962 ~esgd~AAcYhlaR~YEn~g~v~~Av~FfTrAq---------afsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyE 1032 (1416)
T KOG3617|consen  962 EESGDKAACYHLARMYENDGDVVKAVKFFTRAQ---------AFSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYE 1032 (1416)
T ss_pred             HhcccHHHHHHHHHHhhhhHHHHHHHHHHHHHH---------HHHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHH
Confidence             01233333445555666666666665555432         2222232222222111         0000         


Q ss_pred             --hhHHHHHHHHHHcCCChhHHHHHHHhccc--------------CChhhHHHHHHHHHhcCCCCchHHHH----HHHHH
Q 040338          232 --IQIGKALVTMYAEGGSTQKADLAFELMSR--------------RNMISWMVLISAFSQAGVLEKPRFFF----FFVSL  291 (385)
Q Consensus       232 --~~~~~~li~~~~~~g~~~~A~~~~~~m~~--------------~~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l  291 (385)
                        ..-...-+..|.+.|.+.+|+++-=.-.+              .|....+.-.+-++...++++|..++    -|.-.
T Consensus      1033 e~g~~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar~~~~A 1112 (1416)
T KOG3617|consen 1033 ELGGYAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLAREFSGA 1112 (1416)
T ss_pred             HcchhhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence              00112233445555655555554322221              14444555555566666777777666    44455


Q ss_pred             HHHhcccCChhhHHHHHHHHHhcc---c-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcC
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFT---Y-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHY  363 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~---~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g  363 (385)
                      +..|...+ +.-..++-+.|.-..   +     ......+.+.|.++|.+..|-+-|.+.-++      -..++++.+.|
T Consensus      1113 lqlC~~~n-v~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfTQAGdK------l~AMraLLKSG 1185 (1416)
T KOG3617|consen 1113 LQLCKNRN-VRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFTQAGDK------LSAMRALLKSG 1185 (1416)
T ss_pred             HHHHhcCC-CchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHhhhhhH------HHHHHHHHhcC
Confidence            55444333 222333333332211   1     556667788888888888888887766543      12344455555


Q ss_pred             ChHH
Q 040338          364 NTKL  367 (385)
Q Consensus       364 ~~~~  367 (385)
                      +.++
T Consensus      1186 dt~K 1189 (1416)
T KOG3617|consen 1186 DTQK 1189 (1416)
T ss_pred             Ccce
Confidence            5443

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.29  E-value=1.5e-06  Score=48.57  Aligned_cols=35  Identities=31%  Similarity=0.406  Sum_probs=31.5

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCc
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDE   87 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~   87 (385)
                      .+||++|.+|++   .|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~---~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCK---AGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHH---CCCHHHHHHHHHHHHHcCCCCCC
Confidence            479999999888   89999999999999999999874

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.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.27  E-value=5.3e-05  Score=63.74  Aligned_cols=188  Identities=10%  Similarity=-0.137  Sum_probs=126.5

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC----HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchH--
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS----SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVF--  211 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--  211 (385)
                      .....+-.+...+.+.|++++|...|++....  .|+    ..++..+..++...|++++|...++.+.+..+.....  
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~  108 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESR--YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADY  108 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHH
Confidence            45667778888999999999999999999775  333    2456777888999999999999999999876532221  


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CCh-hhHHHHHHHHHhcCCCCchHHHHHH
Q 040338          212 VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNM-ISWMVLISAFSQAGVLEKPRFFFFF  288 (385)
Q Consensus       212 ~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~-~~~~~li~~~~~~g~~~~a~~~~~~  288 (385)
                      ++..+-.++.+.              +...+...|+.++|.+.|+.+.+  |+. ..+..+.......+    ...- ..
T Consensus       109 a~~~~g~~~~~~--------------~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~----~~~~-~~  169 (235)
T TIGR03302       109 AYYLRGLSNYNQ--------------IDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRN----RLAG-KE  169 (235)
T ss_pred             HHHHHHHHHHHh--------------cccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHH----HHHH-HH
Confidence            221111111111              00111223678999999998876  332 22222211110000    0000 12


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  346 (385)
                      ..+...+.+.|++++|...++...+..+     ...+..+..++.+.|++++|.+.++.+..+
T Consensus       170 ~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       170 LYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            2455678899999999999999988754     567888999999999999999999887654

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).

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.27  E-value=0.00084  Score=68.40  Aligned_cols=282  Identities=10%  Similarity=-0.001  Sum_probs=162.5

Q ss_pred             cCChHHHHHHHHHHHHhcc------CCC--chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCC
Q 040338           65 VGNIKMALHLHGLVKKFYF------VSD--ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMP  136 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~------~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~  136 (385)
                      .|+++++..++....+.--      .+.  ......+-..+...|++++|...+++.....                  +
T Consensus       422 ~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~------------------~  483 (903)
T PRK04841        422 QHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAEL------------------P  483 (903)
T ss_pred             CCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC------------------C
Confidence            5777777777776654310      011  1111222234445677777777776543211                  1


Q ss_pred             CCC----cchHHHHHHHHHhCCCchHHHHHHHHHHHC----CC-CCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          137 ERD----LVSWNTMISILTRHGFGFETLCTFIELWNH----GF-GLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       137 ~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                      ..+    ....+.+...+...|++++|...+++....    |- .+-..++..+...+...|+++.|...+++.....-.
T Consensus       484 ~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~  563 (903)
T PRK04841        484 LTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEE  563 (903)
T ss_pred             CccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            112    124455666778899999999999887643    11 111234455666788899999999998887653110


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc------C--ChhhHHHHHHHHHhcCCC
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR------R--NMISWMVLISAFSQAGVL  279 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~------~--~~~~~~~li~~~~~~g~~  279 (385)
                      .               |..........+..+...+...|++++|...+.+...      +  ....+..+...+...|++
T Consensus       564 ~---------------~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~  628 (903)
T PRK04841        564 Q---------------HLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDL  628 (903)
T ss_pred             h---------------ccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCH
Confidence            0               0000000112233444555666788888777766532      1  122333455566677777


Q ss_pred             CchHHHH--H------------HH-----HHHHHhcccCChhhHHHHHHHHHhccc--h----hhHHHHHHHHHccCCHH
Q 040338          280 EKPRFFF--F------------FV-----SLLSGCSHSGPVTKGKHYFTAMAKFTY--T----CYFVCMVDLLGLSGLLG  334 (385)
Q Consensus       280 ~~a~~~~--~------------~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~--~----~~~~~li~~~~~~g~~~  334 (385)
                      ++|.+.+  .            +.     ..+..+...|+.+.|.+.+........  .    .....+..++...|+.+
T Consensus       629 ~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~  708 (903)
T PRK04841        629 DNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFD  708 (903)
T ss_pred             HHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHH
Confidence            7777665  0            00     011233446777777777665443221  1    11345666778888888


Q ss_pred             HHHHHHHhCCCC----C----CcchHHHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          335 EAKKLIDEMPSK----P----TCVIWGALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       335 ~A~~~~~~m~~~----p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      +|...+++....    .    ...+...+..++.+.|+.++|...+.+..+..
T Consensus       709 ~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        709 EAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            888888877541    1    12355666778888899999988888887654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.27  E-value=0.00013  Score=62.19  Aligned_cols=293  Identities=9%  Similarity=-0.032  Sum_probs=142.4

Q ss_pred             hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh--cCChhHHH-
Q 040338           33 LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK--CGAVDYAE-  107 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~--~g~~~~a~-  107 (385)
                      .+++|..++.++.  .|+....|..+..+  +.+..-++.+.+++.--.+. ++-++..-|....-.-+  .|+..+.+ 
T Consensus       166 HYQeAIdvYkrvL~dn~ey~alNVy~ALC--yyKlDYydvsqevl~vYL~q-~pdStiA~NLkacn~fRl~ngr~ae~E~  242 (557)
T KOG3785|consen  166 HYQEAIDVYKRVLQDNPEYIALNVYMALC--YYKLDYYDVSQEVLKVYLRQ-FPDSTIAKNLKACNLFRLINGRTAEDEK  242 (557)
T ss_pred             HHHHHHHHHHHHHhcChhhhhhHHHHHHH--HHhcchhhhHHHHHHHHHHh-CCCcHHHHHHHHHHHhhhhccchhHHHH
Confidence            8899999998877  45555555444322  12267777888888777664 33344444544433333  24332221 


Q ss_pred             -HHHH----------hccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHh
Q 040338          108 -SAFL----------RMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSM  176 (385)
Q Consensus       108 -~~~~----------~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  176 (385)
                       ++-+          .+.+++.+.+ .+-+.|++++-.+.+.-+..--.|+-.|.+.++..+|..+..++.-  ..|-..
T Consensus       243 k~ladN~~~~~~f~~~l~rHNLVvF-rngEgALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~P--ttP~Ey  319 (557)
T KOG3785|consen  243 KELADNIDQEYPFIEYLCRHNLVVF-RNGEGALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLDP--TTPYEY  319 (557)
T ss_pred             HHHHhcccccchhHHHHHHcCeEEE-eCCccHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcCC--CChHHH
Confidence             2221          1222333222 2234455555444332233334455567888999999887766521  222222


Q ss_pred             hHHHHHHH-----hcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHH
Q 040338          177 LYATAFSA-----RASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKA  251 (385)
Q Consensus       177 t~~~ll~~-----~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A  251 (385)
                      ....+..+     ........-|.+.|+..-.++..-|...                     -..++...+.-..++++.
T Consensus       320 ilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIp---------------------GRQsmAs~fFL~~qFddV  378 (557)
T KOG3785|consen  320 ILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIP---------------------GRQSMASYFFLSFQFDDV  378 (557)
T ss_pred             HHHHHHHHHhhhhcCcHHHHHHHHHHHHHhccccccccccc---------------------chHHHHHHHHHHHHHHHH
Confidence            22222221     1122234556666666555554433211                     112222233333345555


Q ss_pred             HHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH------------HHH-HHHHHhcccCChhhHHHHHHHHHhcc
Q 040338          252 DLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF------------FFV-SLLSGCSHSGPVTKGKHYFTAMAKFT  315 (385)
Q Consensus       252 ~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~  315 (385)
                      +-.++.++.   .|...--.+..+++..|.+.+|.++|            +|. .+..+|.+.+.++.|+.++-++...+
T Consensus       379 l~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~~  458 (557)
T KOG3785|consen  379 LTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKTNTPS  458 (557)
T ss_pred             HHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhcCCch
Confidence            555544443   12222223455556666666666655            333 33344555666666655555444433


Q ss_pred             c-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchH
Q 040338          316 Y-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIW  352 (385)
Q Consensus       316 ~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~  352 (385)
                      . ......+..-|-+++.+--|-+.|+++... |++.-|
T Consensus       459 e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~pEnW  497 (557)
T KOG3785|consen  459 ERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTPENW  497 (557)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCcccc
Confidence            3 222233344555667776666777666542 554444

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

Probab=98.25  E-value=0.00024  Score=70.60  Aligned_cols=225  Identities=10%  Similarity=0.036  Sum_probs=149.5

Q ss_pred             CCCchHHHhHHHHHHhcCChhHHHHHHHhccCC-CccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHH
Q 040338           84 VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNP-SLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCT  162 (385)
Q Consensus        84 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  162 (385)
                      |.+...|-..|....+.+++++|.++.++.... +.              .+- +--...|-++++.-...|.-+...++
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~--------------REe-eEKLNiWiA~lNlEn~yG~eesl~kV 1519 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINF--------------REE-EEKLNIWIAYLNLENAYGTEESLKKV 1519 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCc--------------chh-HHHHHHHHHHHhHHHhhCcHHHHHHH
Confidence            445677888888888899999999998876432 11              000 12234688888887778878888899


Q ss_pred             HHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHH
Q 040338          163 FIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMY  242 (385)
Q Consensus       163 ~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~  242 (385)
                      |++..+. .. ....|..|...|.+.+..++|.++++.|.+. +.-...                      .|...+..+
T Consensus      1520 FeRAcqy-cd-~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~----------------------vW~~y~~fL 1574 (1710)
T KOG1070|consen 1520 FERACQY-CD-AYTVHLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRK----------------------VWIMYADFL 1574 (1710)
T ss_pred             HHHHHHh-cc-hHHHHHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhh----------------------HHHHHHHHH
Confidence            9998775 22 2456778888899999999999999999886 223333                      345556666


Q ss_pred             HcCCChhHHHHHHHhccc--C---ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc-
Q 040338          243 AEGGSTQKADLAFELMSR--R---NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-  316 (385)
Q Consensus       243 ~~~g~~~~A~~~~~~m~~--~---~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-  316 (385)
                      .+..+-+.|..++.+..+  |   .+....-.                      +..-.+.|+.++++.+|+......+ 
T Consensus      1575 l~~ne~~aa~~lL~rAL~~lPk~eHv~~Iskf----------------------AqLEFk~GDaeRGRtlfEgll~ayPK 1632 (1710)
T KOG1070|consen 1575 LRQNEAEAARELLKRALKSLPKQEHVEFISKF----------------------AQLEFKYGDAERGRTLFEGLLSAYPK 1632 (1710)
T ss_pred             hcccHHHHHHHHHHHHHhhcchhhhHHHHHHH----------------------HHHHhhcCCchhhHHHHHHHHhhCcc
Confidence            666677788888776554  2   12221112                      2223455667777777777777776 


Q ss_pred             -hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---C--CcchHHHHHHHHHhcCChHHHHH
Q 040338          317 -TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---P--TCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       317 -~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p--~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                       ...|+.+|+.-.+.|+.+.+..+|++....   |  -...|.-.+..--++|+-..+..
T Consensus      1633 RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~vE~ 1692 (1710)
T KOG1070|consen 1633 RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEKNVEY 1692 (1710)
T ss_pred             chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchhhHHH
Confidence             777888888888888888888888877663   1  12356666666566666544333

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.24  E-value=0.00011  Score=66.39  Aligned_cols=231  Identities=13%  Similarity=0.092  Sum_probs=155.3

Q ss_pred             HHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CH
Q 040338           97 HVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SS  175 (385)
Q Consensus        97 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~  175 (385)
                      +.+.|++.+|.-.|+...+.+                   +.+...|-.|--....+++-..|+..+++..+  +.| |.
T Consensus       295 lm~nG~L~~A~LafEAAVkqd-------------------P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~--LdP~Nl  353 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD-------------------PQHAEAWQKLGITQAENENEQNAISALRRCLE--LDPTNL  353 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC-------------------hHHHHHHHHhhhHhhhccchHHHHHHHHHHHh--cCCccH
Confidence            445677777777777766655                   35778898888888899998899999998887  466 56


Q ss_pred             hhHHHHHHHhcCccCccchhhHHHHHHHhCC-------------------CCchHHHHHHHHHHHhcCCCC-CCchhhHH
Q 040338          176 MLYATAFSARASVYDLEWGPHLHSRVVHMEP-------------------SLDVFVGSGLIDMYLKCGCNG-IESSIQIG  235 (385)
Q Consensus       176 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-------------------~~~~~~~~~li~~~~~~g~~~-~~~~~~~~  235 (385)
                      ...-.|.-.|...|.-..|.+.++.-+...+                   .++...+..+-..|...++.. ..+|..+.
T Consensus       354 eaLmaLAVSytNeg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ  433 (579)
T KOG1125|consen  354 EALMALAVSYTNEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQ  433 (579)
T ss_pred             HHHHHHHHHHhhhhhHHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHH
Confidence            6777777788888888888888888765432                   134445555555555544333 23666677


Q ss_pred             HHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHH
Q 040338          236 KALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMA  312 (385)
Q Consensus       236 ~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  312 (385)
                      ..|.-.|.-.|++++|.+.|+....  | |-..||.|...++...+..                      +|+.-|.+..
T Consensus       434 ~~LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~----------------------EAIsAY~rAL  491 (579)
T KOG1125|consen  434 SGLGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSE----------------------EAISAYNRAL  491 (579)
T ss_pred             hhhHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccH----------------------HHHHHHHHHH
Confidence            7788888888888888888887754  4 5567777777776665554                      4555666666


Q ss_pred             hccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC---C---------CCcchHHHHHHHHHhcCChHHHHH
Q 040338          313 KFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS---K---------PTCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       313 ~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~---------p~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      +..+  +.+..-|.-+|...|.+.+|.+.|-+...   +         ++...|.+|=.++.-.+..|.+.+
T Consensus       492 qLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~  563 (579)
T KOG1125|consen  492 QLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQE  563 (579)
T ss_pred             hcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHH
Confidence            6555  44444566677777777777776644322   1         223466666666666666654433

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.22  E-value=0.00026  Score=63.53  Aligned_cols=147  Identities=10%  Similarity=-0.008  Sum_probs=90.5

Q ss_pred             HHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHH-------------------HHHHHHH
Q 040338          235 GKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFF-------------------FFVSLLS  293 (385)
Q Consensus       235 ~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~-------------------~~~~l~~  293 (385)
                      ...+.++..+..+++.|++-++...+  .++.-++....+|...|.+.+.....                   .+..+..
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~  306 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELATDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGN  306 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHhhhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhh
Confidence            34566666666677777777766554  23333444555566655554443333                   3444555


Q ss_pred             HhcccCChhhHHHHHHHHHhccc-hhhHH---------------------------HHHHHHHccCCHHHHHHHHHhCCC
Q 040338          294 GCSHSGPVTKGKHYFTAMAKFTY-TCYFV---------------------------CMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       294 ~~~~~~~~~~a~~~~~~~~~~~~-~~~~~---------------------------~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      +|.+.++.+.++..|.+...... +...+                           .=...+.+.|++..|++.|.++..
T Consensus       307 a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIk  386 (539)
T KOG0548|consen  307 AYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIK  386 (539)
T ss_pred             hhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHh
Confidence            66666777777777776544322 11111                           114456677888888888888766


Q ss_pred             C-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          346 K-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       346 ~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      + | |...|..-.-+|.+.|.+..|+.-.+...+++|+
T Consensus       387 r~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~  424 (539)
T KOG0548|consen  387 RDPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPN  424 (539)
T ss_pred             cCCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCch
Confidence            4 4 5667888888888888888888777777776654

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.21  E-value=5.4e-05  Score=58.12  Aligned_cols=84  Identities=8%  Similarity=-0.185  Sum_probs=51.4

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...|+...... +.+...|..+..++.+.|++++|...|++....+                   +.+...+.
T Consensus        37 ~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-------------------p~~~~a~~   96 (144)
T PRK15359         37 EGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-------------------ASHPEPVY   96 (144)
T ss_pred             cCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-------------------CCCcHHHH
Confidence            566666666666666543 2355566666666666666666666666655544                   34555666


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      .+..++.+.|++++|...|+...+
T Consensus        97 ~lg~~l~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359         97 QTGVCLKMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            666666666666666666666655

>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=98.18  E-value=2.6e-05  Score=62.09  Aligned_cols=120  Identities=10%  Similarity=-0.014  Sum_probs=90.7

Q ss_pred             hhHHHHHhhh--CCCChhhHHHHHHHHHhh--hccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHH
Q 040338           35 DDDYRVFCDI--GPRYLFTYNTMINGGVRC--LCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF  110 (385)
Q Consensus        35 ~~A~~~~~~~--~~~~~~~~~~li~~~~~~--~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~  110 (385)
                      .--...|+..  ...|-.+|..+|..|...  .++|+++-....+..|.+.|+.-|..+|+.||+.+=+ |.+- ...+|
T Consensus        31 ~~~~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv-p~n~f  108 (228)
T PF06239_consen   31 APHEELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV-PRNFF  108 (228)
T ss_pred             cchHHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc-cccHH
Confidence            3345566665  477889999999999864  4589999999999999999999999999999998864 3221 11122


Q ss_pred             HhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccC
Q 040338          111 LRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYD  190 (385)
Q Consensus       111 ~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~  190 (385)
                      +.                                 +..-|  -.+-+-|++++++|...|+-||..|+..+++.+++.+.
T Consensus       109 Q~---------------------------------~F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  109 QA---------------------------------EFMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HH---------------------------------HhccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            11                                 11111  23456789999999999999999999999999988765


Q ss_pred             c
Q 040338          191 L  191 (385)
Q Consensus       191 ~  191 (385)
                      .
T Consensus       154 p  154 (228)
T PF06239_consen  154 P  154 (228)
T ss_pred             H
Confidence            3

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

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=98.18  E-value=0.0038  Score=57.63  Aligned_cols=202  Identities=10%  Similarity=-0.022  Sum_probs=116.4

Q ss_pred             CCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHH
Q 040338            7 LKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALH   73 (385)
Q Consensus         7 ~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~   73 (385)
                      .+++..+....+++++.-......+.          +-++|......-.   ..+.+.|+.+--.+..   .+++++|++
T Consensus        20 ~kQYkkgLK~~~~iL~k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~---dK~Y~eaiK   96 (700)
T KOG1156|consen   20 TKQYKKGLKLIKQILKKFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRS---DKKYDEAIK   96 (700)
T ss_pred             HHHHHhHHHHHHHHHHhCCccchhHHhccchhhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhh---hhhHHHHHH
Confidence            35666677777777765433333333          6666666655433   3345566655444333   678888888


Q ss_pred             HHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc---cccc---------cchHHHHHHhcCCC-----
Q 040338           74 LHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL---FCWK---------FGIIRLLIMFQKMP-----  136 (385)
Q Consensus        74 ~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~~~~---------~~~~~a~~~~~~~~-----  136 (385)
                      .+....+.+ +-|...+.-+--.=++.|+++.......+..+..+   ..|-         |+...|..++++..     
T Consensus        97 cy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~  175 (700)
T KOG1156|consen   97 CYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNT  175 (700)
T ss_pred             HHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            888887764 33666777666666666777666666555543322   2222         55555554444331     


Q ss_pred             CCCcchHHHHH------HHHHhCCCchHHHHHHHHHHHCCCCCCHhhH-HHHHHHhcCccCccchhhHHHHHHHhCCCCc
Q 040338          137 ERDLVSWNTMI------SILTRHGFGFETLCTFIELWNHGFGLSSMLY-ATAFSARASVYDLEWGPHLHSRVVHMEPSLD  209 (385)
Q Consensus       137 ~~~~~~~~~li------~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  209 (385)
                      .|+...|.-..      ......|.+++|++.+..-...  ..|...| .+-...+.+.+++++|..++..++..+  ||
T Consensus       176 ~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~--i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rn--Pd  251 (700)
T KOG1156|consen  176 SPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ--IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERN--PD  251 (700)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH--HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhC--ch
Confidence            24544443322      3445667777777776654332  2233333 234555677888888888888888764  55


Q ss_pred             hHHHHHH
Q 040338          210 VFVGSGL  216 (385)
Q Consensus       210 ~~~~~~l  216 (385)
                      ..-|...
T Consensus       252 n~~Yy~~  258 (700)
T KOG1156|consen  252 NLDYYEG  258 (700)
T ss_pred             hHHHHHH
Confidence            5555443

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

Probab=98.18  E-value=2.4e-06  Score=46.24  Aligned_cols=31  Identities=32%  Similarity=0.398  Sum_probs=26.9

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCC
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGF  171 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  171 (385)
                      ++||++|++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4789999999999999999999999988774

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.16  E-value=4.6e-06  Score=46.23  Aligned_cols=33  Identities=24%  Similarity=0.354  Sum_probs=28.4

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCC
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVS   85 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~   85 (385)
                      .+||++|.++++   .|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~---~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAK---AGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHH---CCCHHHHHHHHHHHHHhCCCC
Confidence            588999999766   899999999999999888877

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

Probab=98.13  E-value=0.00024  Score=61.83  Aligned_cols=148  Identities=9%  Similarity=-0.101  Sum_probs=77.7

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLR  112 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  112 (385)
                      +..+|...|++..--|+.+...|=.--.-.+..|+.+....+.+.+.... .-+...|-.-........+++.|+.+-++
T Consensus       247 dn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK  325 (564)
T KOG1174|consen  247 DYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEK  325 (564)
T ss_pred             CchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHH
Confidence            77777777776653333322221110001122677777777777766532 12333344444445556777777777777


Q ss_pred             ccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCc
Q 040338          113 MLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDL  191 (385)
Q Consensus       113 m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~  191 (385)
                      ..+.+.                   .++..|-.--..+...+++++|.=.|+..+.  +.| +...|.-|+.+|...|.+
T Consensus       326 ~I~~~~-------------------r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~--Lap~rL~~Y~GL~hsYLA~~~~  384 (564)
T KOG1174|consen  326 CIDSEP-------------------RNHEALILKGRLLIALERHTQAVIAFRTAQM--LAPYRLEIYRGLFHSYLAQKRF  384 (564)
T ss_pred             HhccCc-------------------ccchHHHhccHHHHhccchHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhhchH
Confidence            665542                   3333333333445555666666666655544  233 455666666666666666


Q ss_pred             cchhhHHHHHH
Q 040338          192 EWGPHLHSRVV  202 (385)
Q Consensus       192 ~~a~~~~~~~~  202 (385)
                      .+|.-+-+...
T Consensus       385 kEA~~~An~~~  395 (564)
T KOG1174|consen  385 KEANALANWTI  395 (564)
T ss_pred             HHHHHHHHHHH
Confidence            55554444433

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.12  E-value=0.00016  Score=58.70  Aligned_cols=114  Identities=6%  Similarity=-0.034  Sum_probs=62.5

Q ss_pred             hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHH-HhcCC--hhHH
Q 040338           33 LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMH-VKCGA--VDYA  106 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~-~~~g~--~~~a  106 (385)
                      +.+++...++...   +.|...|..+-..+..   .|+++.|...++...+.. +-+...+..+..++ ...|+  .++|
T Consensus        54 ~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~---~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         54 TPEAQLQALQDKIRANPQNSEQWALLGEYYLW---RNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             hHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            4444444444332   3345555555555444   566666666666666543 22455555555543 44454  3666


Q ss_pred             HHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          107 ESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       107 ~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      .+++++..+.+                   +.+..++..+...+.+.|++++|+..|+++.+.
T Consensus       130 ~~~l~~al~~d-------------------P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        130 REMIDKALALD-------------------ANEVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHHhC-------------------CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            66666665554                   245555666666666666666666666666554

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.11  E-value=0.0051  Score=62.74  Aligned_cols=214  Identities=10%  Similarity=-0.012  Sum_probs=141.2

Q ss_pred             HHHHhCCCchHHHHHHHHHHHCCCCCCH----hhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          148 SILTRHGFGFETLCTFIELWNHGFGLSS----MLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       148 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      ..+...|++++|...+++....--..+.    ...+.+...+...|+++.|...+++.....-......           
T Consensus       460 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~-----------  528 (903)
T PRK04841        460 QVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYH-----------  528 (903)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchH-----------
Confidence            4556789999999999988763111121    2344555667789999999999988876422111100           


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-------CC----hhhHHHHHHHHHhcCCCCchHHHH------
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-------RN----MISWMVLISAFSQAGVLEKPRFFF------  286 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~~----~~~~~~li~~~~~~g~~~~a~~~~------  286 (385)
                            +...++..+...+...|+++.|...+++..+       ++    ...+..+...+...|++++|...+      
T Consensus       529 ------~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~  602 (903)
T PRK04841        529 ------YALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEV  602 (903)
T ss_pred             ------HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHh
Confidence                  1112335566677889999999998877653       11    123444556677789999987776      


Q ss_pred             -----------HHHHHHHHhcccCChhhHHHHHHHHHhccc----hhhH-----HHHHHHHHccCCHHHHHHHHHhCCCC
Q 040338          287 -----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----TCYF-----VCMVDLLGLSGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       287 -----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~-----~~li~~~~~~g~~~~A~~~~~~m~~~  346 (385)
                                 .+..+.......|+.+.|...++.......    ...+     ...+..+...|+.+.|.+++......
T Consensus       603 ~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~  682 (903)
T PRK04841        603 LSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKP  682 (903)
T ss_pred             hhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCC
Confidence                       344456667788999999999888755322    1111     11234455689999999998876653


Q ss_pred             --CCc----chHHHHHHHHHhcCChHHHHHHHHHHHhc
Q 040338          347 --PTC----VIWGALLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       347 --p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                        ...    ..+..+..++...|++++|...+++....
T Consensus       683 ~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~  720 (903)
T PRK04841        683 EFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNEN  720 (903)
T ss_pred             CCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence              111    11346777889999999999999988764

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

Probab=98.10  E-value=0.00049  Score=68.53  Aligned_cols=187  Identities=10%  Similarity=0.152  Sum_probs=126.7

Q ss_pred             hHHHHHHHhcCccCccchhhHHHHHHHh-CCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHH
Q 040338          177 LYATAFSARASVYDLEWGPHLHSRVVHM-EPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAF  255 (385)
Q Consensus       177 t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~  255 (385)
                      .|-.-+......++.++|.++.++.+.. ++.-...-                   ...|.++++.-..-|.-+...++|
T Consensus      1460 ~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEK-------------------LNiWiA~lNlEn~yG~eesl~kVF 1520 (1710)
T KOG1070|consen 1460 LWIRYMAFHLELSEIEKARKIAERALKTINFREEEEK-------------------LNIWIAYLNLENAYGTEESLKKVF 1520 (1710)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHH-------------------HHHHHHHHhHHHhhCcHHHHHHHH
Confidence            3334444455666666666666666543 22111111                   123344444444445555566666


Q ss_pred             HhcccC-C-hhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc----h
Q 040338          256 ELMSRR-N-MISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----T  317 (385)
Q Consensus       256 ~~m~~~-~-~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~  317 (385)
                      ++..+- | -..|..|...|.+.+..++|-+++            .|...+....+..+-+.|..++.+..+.-+    .
T Consensus      1521 eRAcqycd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv 1600 (1710)
T KOG1070|consen 1521 ERACQYCDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHV 1600 (1710)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhH
Confidence            665542 2 245555666666666666666666            677777777777777888888888776555    6


Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ......+..-.+.|+.+.+..+|+..... | -...|+..|..-.++|+.+.++.+|++.+.++..+
T Consensus      1601 ~~IskfAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1601 EFISKFAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHHHHHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            66777788888999999999999998875 3 45689999999999999999999999999888764

>PLN02789 farnesyltranstransferase

Probab=98.09  E-value=0.0027  Score=55.60  Aligned_cols=221  Identities=8%  Similarity=-0.083  Sum_probs=138.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcC-ChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCG-AVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      .++.++|+.+.+++++... -+..+|+..-.++...| ++++++..++++.+.+                   +.+..+|
T Consensus        50 ~e~serAL~lt~~aI~lnP-~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-------------------pknyqaW  109 (320)
T PLN02789         50 DERSPRALDLTADVIRLNP-GNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-------------------PKNYQIW  109 (320)
T ss_pred             CCCCHHHHHHHHHHHHHCc-hhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-------------------CcchHHh
Confidence            6789999999999998642 24456666666666666 5789999998887766                   3566678


Q ss_pred             HHHHHHHHhCCCc--hHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHH
Q 040338          144 NTMISILTRHGFG--FETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYL  221 (385)
Q Consensus       144 ~~li~~~~~~~~~--~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  221 (385)
                      +-.-..+.+.|+.  ++++.+++++.+.. +-|.+.|+....++.+.|+++++++.++++++.++. +..+|+.....+.
T Consensus       110 ~~R~~~l~~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~  187 (320)
T PLN02789        110 HHRRWLAEKLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVIT  187 (320)
T ss_pred             HHHHHHHHHcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHH
Confidence            7665556666653  67888898888752 227788888888888889999999999999988653 3344433332222


Q ss_pred             hcCCCCCCchhhHHHHHHHHHHcCCC----hhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q 040338          222 KCGCNGIESSIQIGKALVTMYAEGGS----TQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSG  294 (385)
Q Consensus       222 ~~g~~~~~~~~~~~~~li~~~~~~g~----~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~  294 (385)
                      +.|.                   .|+    .+++++...+..+  | |..+|+-+...+...+..               
T Consensus       188 ~~~~-------------------l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~---------------  233 (320)
T PLN02789        188 RSPL-------------------LGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEA---------------  233 (320)
T ss_pred             hccc-------------------cccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcc---------------
Confidence            2210                   112    2455666555543  3 667777777777653321               


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC------------------CHHHHHHHHHhCC
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG------------------LLGEAKKLIDEMP  344 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g------------------~~~~A~~~~~~m~  344 (385)
                         .+...++.+++.+....++  ......|++.|+...                  ..++|.++++.+.
T Consensus       234 ---l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        234 ---LVSDPEVSSVCLEVLSKDSNHVFALSDLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSELE  300 (320)
T ss_pred             ---cccchhHHHHHHHhhcccCCcHHHHHHHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHHH
Confidence               0122234444444444333  455555666665421                  3466888877773

>PLN02789 farnesyltranstransferase

Probab=98.07  E-value=0.0028  Score=55.47  Aligned_cols=225  Identities=10%  Similarity=-0.011  Sum_probs=143.7

Q ss_pred             HHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCC-CchHHHHHHHHHHHCCCCCCH
Q 040338           97 HVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHG-FGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus        97 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~g~~p~~  175 (385)
                      +...++.++|+.+.+++.+.+                   +.+..+|+..-.++...| +++++++.++++.+...+ +.
T Consensus        47 l~~~e~serAL~lt~~aI~ln-------------------P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-ny  106 (320)
T PLN02789         47 YASDERSPRALDLTADVIRLN-------------------PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NY  106 (320)
T ss_pred             HHcCCCCHHHHHHHHHHHHHC-------------------chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-ch
Confidence            334567778888887776555                   345557776666666667 579999999999876332 34


Q ss_pred             hhHHHHHHHhcCccC--ccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHH
Q 040338          176 MLYATAFSARASVYD--LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADL  253 (385)
Q Consensus       176 ~t~~~ll~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~  253 (385)
                      .+|+.--..+.+.|+  .+++..+.+.+++...                       .+..+|+...-.+...|+++++++
T Consensus       107 qaW~~R~~~l~~l~~~~~~~el~~~~kal~~dp-----------------------kNy~AW~~R~w~l~~l~~~~eeL~  163 (320)
T PLN02789        107 QIWHHRRWLAEKLGPDAANKELEFTRKILSLDA-----------------------KNYHAWSHRQWVLRTLGGWEDELE  163 (320)
T ss_pred             HHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCc-----------------------ccHHHHHHHHHHHHHhhhHHHHHH
Confidence            445543333334444  2566777777776543                       244556666667777789999999


Q ss_pred             HHHhccc---CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHH
Q 040338          254 AFELMSR---RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLG  328 (385)
Q Consensus       254 ~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~  328 (385)
                      .++++.+   .|...|+.....+.+.|....-               ....+.......++....+  ...|+-+...+.
T Consensus       164 ~~~~~I~~d~~N~sAW~~R~~vl~~~~~l~~~---------------~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~  228 (320)
T PLN02789        164 YCHQLLEEDVRNNSAWNQRYFVITRSPLLGGL---------------EAMRDSELKYTIDAILANPRNESPWRYLRGLFK  228 (320)
T ss_pred             HHHHHHHHCCCchhHHHHHHHHHHhccccccc---------------cccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHh
Confidence            9999987   3556666655555443221110               0123456667766666666  777777777776


Q ss_pred             cc----CCHHHHHHHHHhCCC-C-CCcchHHHHHHHHHhcC------------------ChHHHHHHHHHHHhcc
Q 040338          329 LS----GLLGEAKKLIDEMPS-K-PTCVIWGALLGACCSHY------------------NTKLAELVMRNLLQLD  379 (385)
Q Consensus       329 ~~----g~~~~A~~~~~~m~~-~-p~~~~~~~li~~~~~~g------------------~~~~a~~~~~~~~~~~  379 (385)
                      ..    ++..+|.+.+.+... . .+......|+..|+...                  ..++|.++++.+.+.+
T Consensus       229 ~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~d  303 (320)
T PLN02789        229 DDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSELEVAD  303 (320)
T ss_pred             cCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHHHhhC
Confidence            63    445678888887655 3 35567788888888642                  2367888888885433

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.06  E-value=0.00053  Score=67.09  Aligned_cols=213  Identities=9%  Similarity=-0.025  Sum_probs=149.4

Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhh-HHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSML-YATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                      +.+...+..|+..+...+++++|.++.+...+.  .|+... |-.+...+...++...+..+  .+.+.  .+...-|+.
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~--~~~~~~~~~  101 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL--NLIDS--FSQNLKWAI  101 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh--hhhhh--cccccchhH
Confidence            456778999999999999999999999977664  665544 33344467777777777766  33332  222222233


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHHHHHHHH
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFFFFVSLL  292 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~  292 (385)
                      +-..|...|+.  .-+..++-.+..+|-+.|+.++|..+|+++.+   .|....|.+...|... ++++|++++  ...+
T Consensus       102 ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~--~KAV  176 (906)
T PRK14720        102 VEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYL--KKAI  176 (906)
T ss_pred             HHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHH--HHHH
Confidence            33333333332  23445788899999999999999999999987   3778889999999998 999999886  3333


Q ss_pred             HHhcccCChhhHHHHHHHHHhccc----------------------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CC
Q 040338          293 SGCSHSGPVTKGKHYFTAMAKFTY----------------------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PT  348 (385)
Q Consensus       293 ~~~~~~~~~~~a~~~~~~~~~~~~----------------------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~  348 (385)
                      ..+....++..+..+|.++....+                      ..++..+-..|-..++++++..+|+.+.+-  .|
T Consensus       177 ~~~i~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n  256 (906)
T PRK14720        177 YRFIKKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKN  256 (906)
T ss_pred             HHHHhhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcc
Confidence            446666778888888888877655                      223333446677778888888888888763  45


Q ss_pred             cchHHHHHHHHH
Q 040338          349 CVIWGALLGACC  360 (385)
Q Consensus       349 ~~~~~~li~~~~  360 (385)
                      .....-++.+|.
T Consensus       257 ~~a~~~l~~~y~  268 (906)
T PRK14720        257 NKAREELIRFYK  268 (906)
T ss_pred             hhhHHHHHHHHH
Confidence            556667777776

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.05  E-value=0.0025  Score=56.95  Aligned_cols=195  Identities=12%  Similarity=-0.073  Sum_probs=130.6

Q ss_pred             hhhhHHHHHhhhC------CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHH
Q 040338           33 LIDDDYRVFCDIG------PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYA  106 (385)
Q Consensus        33 ~~~~A~~~~~~~~------~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a  106 (385)
                      ++.+++..-+.++      .|+...+...+.+...    .-.......+..+... ..-...-|..-+..| ..|+.++|
T Consensus       252 RIa~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~----~~~~~~~~~~~~~~~~-~~~~aa~YG~A~~~~-~~~~~d~A  325 (484)
T COG4783         252 RIADLRNRAEQSPPYNKLDSPDFQLARARIRAKYE----ALPNQQAADLLAKRSK-RGGLAAQYGRALQTY-LAGQYDEA  325 (484)
T ss_pred             HHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhc----cccccchHHHHHHHhC-ccchHHHHHHHHHHH-HhcccchH
Confidence            8888888888777      3445556666665433    2222222222223222 111233344444433 67888888


Q ss_pred             HHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH-hhHHHHHHHh
Q 040338          107 ESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS-MLYATAFSAR  185 (385)
Q Consensus       107 ~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~ll~~~  185 (385)
                      +..++.+...-                   +.|+.-+......+.+.++.++|.+.++++...  .|+. ...-.+..++
T Consensus       326 ~~~l~~L~~~~-------------------P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~al  384 (484)
T COG4783         326 LKLLQPLIAAQ-------------------PDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQAL  384 (484)
T ss_pred             HHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHH
Confidence            88888765433                   345556666778899999999999999999874  6763 4445677788


Q ss_pred             cCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          186 ASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       186 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                      .+.|+..+|+.+++...... +-|+..|..|..+|...|+     ....-.+-..+|...|+++.|+..+....+
T Consensus       385 l~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~-----~~~a~~A~AE~~~~~G~~~~A~~~l~~A~~  453 (484)
T COG4783         385 LKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGN-----RAEALLARAEGYALAGRLEQAIIFLMRASQ  453 (484)
T ss_pred             HhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCc-----hHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            99999999999999887764 4677788888888887773     344555666777777888888877766654

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.04  E-value=0.00061  Score=66.68  Aligned_cols=234  Identities=8%  Similarity=-0.071  Sum_probs=128.8

Q ss_pred             CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC-chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccch
Q 040338           47 RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD-ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGI  125 (385)
Q Consensus        47 ~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~  125 (385)
                      .+...|..|+..+..   .+++++|.++.+...+.  .|+ ...|-.+...+.+.++.+++..+  .             
T Consensus        29 ~n~~a~~~Li~~~~~---~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv--~-------------   88 (906)
T PRK14720         29 SKFKELDDLIDAYKS---ENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL--N-------------   88 (906)
T ss_pred             chHHHHHHHHHHHHh---cCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh--h-------------
Confidence            345567788887655   78888888888866554  444 34444444566666766655444  2             


Q ss_pred             HHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          126 IRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       126 ~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                                          ++.......++.-+..+...|.+.  .-+...+..+..+|-+.|+.+++..+++++++..
T Consensus        89 --------------------~l~~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D  146 (906)
T PRK14720         89 --------------------LIDSFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD  146 (906)
T ss_pred             --------------------hhhhcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC
Confidence                                222222233332222333333321  1122344444445555555555555555555544


Q ss_pred             CCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChh---hHHHHHHHHHhcCCCCch
Q 040338          206 PSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMI---SWMVLISAFSQAGVLEKP  282 (385)
Q Consensus       206 ~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~---~~~~li~~~~~~g~~~~a  282 (385)
                       +-+..+.|-+...|...   +.......+...+..+....++.++.++|.++..-++.   .+-.+.......-...++
T Consensus       147 -~~n~~aLNn~AY~~ae~---dL~KA~~m~~KAV~~~i~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~  222 (906)
T PRK14720        147 -RDNPEIVKKLATSYEEE---DKEKAITYLKKAIYRFIKKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRL  222 (906)
T ss_pred             -cccHHHHHHHHHHHHHh---hHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchh
Confidence             23344444444444443   22333333344444566667888999999988874333   333333333332223333


Q ss_pred             HHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHH
Q 040338          283 RFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLG  328 (385)
Q Consensus       283 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~  328 (385)
                      ..  ++-.+-..|....+++++..+++.+.+...  .....-++.+|.
T Consensus       223 ~~--~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        223 VG--LLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             HH--HHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH
Confidence            32  456666778889999999999999999888  444455565554

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.04  E-value=8.1e-05  Score=57.12  Aligned_cols=109  Identities=5%  Similarity=-0.149  Sum_probs=90.0

Q ss_pred             HHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHh
Q 040338           73 HLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTR  152 (385)
Q Consensus        73 ~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~  152 (385)
                      .+++...+.  .|+  .+..+...+...|++++|...|++....+                   +.+...|..+..++.+
T Consensus        14 ~~~~~al~~--~p~--~~~~~g~~~~~~g~~~~A~~~~~~al~~~-------------------P~~~~a~~~lg~~~~~   70 (144)
T PRK15359         14 DILKQLLSV--DPE--TVYASGYASWQEGDYSRAVIDFSWLVMAQ-------------------PWSWRAHIALAGTWMM   70 (144)
T ss_pred             HHHHHHHHc--CHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------------------CCcHHHHHHHHHHHHH
Confidence            445555543  333  35567788889999999999999987766                   4688899999999999


Q ss_pred             CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          153 HGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       153 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      .|++++|...|+..... -+.+...+..+..++...|+.++|+..++..++..
T Consensus        71 ~g~~~~A~~~y~~Al~l-~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~  122 (144)
T PRK15359         71 LKEYTTAINFYGHALML-DASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMS  122 (144)
T ss_pred             HhhHHHHHHHHHHHHhc-CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999999999999975 23377888889999999999999999999998865

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.01  E-value=0.00031  Score=54.09  Aligned_cols=124  Identities=14%  Similarity=0.102  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHcCCChhHHHHHHHhcccCChhh-HHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHH
Q 040338          234 IGKALVTMYAEGGSTQKADLAFELMSRRNMIS-WMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMA  312 (385)
Q Consensus       234 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~-~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  312 (385)
                      .|..++..+. .++...+...++.+.+.+..+ |..+.                 .-.+...+...|++++|...|+.+.
T Consensus        14 ~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A-----------------~l~lA~~~~~~g~~~~A~~~l~~~~   75 (145)
T PF09976_consen   14 LYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALA-----------------ALQLAKAAYEQGDYDEAKAALEKAL   75 (145)
T ss_pred             HHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHH-----------------HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4455555553 677888888888777633222 33322                 2234455667788888888898888


Q ss_pred             hccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          313 KFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       313 ~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      ....     ......+...+...|++++|+..++..... .....+......|.+.|++++|...|++.
T Consensus        76 ~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   76 ANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             hhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            7664     334455788889999999999999886654 34456777888999999999999999874

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

Probab=98.01  E-value=0.00021  Score=54.24  Aligned_cols=92  Identities=13%  Similarity=-0.041  Sum_probs=64.1

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|.+.++.+.+.+ +.+...+..+...+.+.|++++|...+++..+.+                   +.+..++.
T Consensus        30 ~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-------------------p~~~~~~~   89 (135)
T TIGR02552        30 QGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-------------------PDDPRPYF   89 (135)
T ss_pred             cccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-------------------CCChHHHH
Confidence            677888888887777654 3366777777777777788888887777765544                   35566666


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLY  178 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~  178 (385)
                      .+...+...|++++|...|+...+.  .|+...+
T Consensus        90 ~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~  121 (135)
T TIGR02552        90 HAAECLLALGEPESALKALDLAIEI--CGENPEY  121 (135)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--ccccchH
Confidence            6777777778888888877777664  4544443

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

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

Probab=98.00  E-value=8.5e-06  Score=44.00  Aligned_cols=31  Identities=16%  Similarity=0.265  Sum_probs=25.9

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          350 VIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       350 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      +||++++++|++.|++++|.+++++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4788888888888888888888888888764

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.

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.00  E-value=0.0002  Score=58.16  Aligned_cols=121  Identities=10%  Similarity=-0.046  Sum_probs=100.8

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .++.+++...++...+.. +.+...|..+...|...|+.++|...|++..+.+                   +.+...+.
T Consensus        52 ~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-------------------P~~~~~~~  111 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLR-------------------GENAELYA  111 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------------------CCCHHHHH
Confidence            466677887888777765 5588999999999999999999999999887766                   46777888


Q ss_pred             HHHHHH-HhCCC--chHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          145 TMISIL-TRHGF--GFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       145 ~li~~~-~~~~~--~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                      .+..++ ...|+  .++|.+++++..+.  .| +...+..+...+.+.|++++|+..|+.+++...+
T Consensus       112 ~lA~aL~~~~g~~~~~~A~~~l~~al~~--dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~  176 (198)
T PRK10370        112 ALATVLYYQAGQHMTPQTREMIDKALAL--DANEVTALMLLASDAFMQADYAQAIELWQKVLDLNSP  176 (198)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHHHh--CCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            888764 67777  59999999999986  44 6678888888999999999999999999988653

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

Probab=98.00  E-value=6.2e-05  Score=53.13  Aligned_cols=80  Identities=13%  Similarity=-0.094  Sum_probs=67.7

Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCC-CCCHhhHHHHHHHhcCcc--------CccchhhHHHHHHHhCCCCchHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGF-GLSSMLYATAFSARASVY--------DLEWGPHLHSRVVHMEPSLDVFVG  213 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~  213 (385)
                      -...|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        .+...+.+|+.|+..+++|+..+|
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etY  107 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETY  107 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHH
Confidence            34567777778999999999999999999 999999999999877543        244667899999999999999999


Q ss_pred             HHHHHHHHh
Q 040338          214 SGLIDMYLK  222 (385)
Q Consensus       214 ~~li~~~~~  222 (385)
                      +.++..+.+
T Consensus       108 nivl~~Llk  116 (120)
T PF08579_consen  108 NIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHH
Confidence            988887765

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 [, , ].

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.00  E-value=0.004  Score=56.19  Aligned_cols=352  Identities=9%  Similarity=-0.100  Sum_probs=210.1

Q ss_pred             ccCCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhC--CCC-hhhHHHHHHHHHhhhccCChHH
Q 040338            5 GSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIG--PRY-LFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      -.+|+++.|...|...+.-... +..++           ++++|.+=-.+-.  .|+ ...|+-.-.++.-   .|++++
T Consensus        13 ~s~~d~~~ai~~~t~ai~l~p~-nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~w~kgy~r~Gaa~~~---lg~~~e   88 (539)
T KOG0548|consen   13 FSSGDFETAIRLFTEAIMLSPT-NHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDWAKGYSRKGAALFG---LGDYEE   88 (539)
T ss_pred             cccccHHHHHHHHHHHHccCCC-ccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCchhhHHHHhHHHHHh---cccHHH
Confidence            3579999999999998876544 44444           5555544322222  444 3456666555444   899999


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcC---ChhHHHHHHHhc---------------------cCCCccccc----
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCG---AVDYAESAFLRM---------------------LNPSLFCWK----  122 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~m---------------------~~~~~~~~~----  122 (385)
                      |+.-|.+-.+.. +.+...++-|.+++....   +.-.--.++...                     .+.++-..+    
T Consensus        89 A~~ay~~GL~~d-~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~l~  167 (539)
T KOG0548|consen   89 AILAYSEGLEKD-PSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLYLN  167 (539)
T ss_pred             HHHHHHHHhhcC-CchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhcccc
Confidence            999998888763 446677777777762110   000000000000                     001110000    


Q ss_pred             -cchHHHHHHhcCC----------------CCC------------C----------cchHHHHHHHHHhCCCchHHHHHH
Q 040338          123 -FGIIRLLIMFQKM----------------PER------------D----------LVSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus       123 -~~~~~a~~~~~~~----------------~~~------------~----------~~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                       ..+..+...+...                .+|            |          ..-...+.+...+..+++.+++-+
T Consensus       168 d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q~y  247 (539)
T KOG0548|consen  168 DPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQHY  247 (539)
T ss_pred             cHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHH
Confidence             1111111111111                011            0          012445667777778888888888


Q ss_pred             HHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHH
Q 040338          164 IELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA  243 (385)
Q Consensus       164 ~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~  243 (385)
                      ....+..  -+..-++..-.++...|........-+..++.|. -...-|+-+-.++.+.|               .+|.
T Consensus       248 ~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gr-e~rad~klIak~~~r~g---------------~a~~  309 (539)
T KOG0548|consen  248 AKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGR-ELRADYKLIAKALARLG---------------NAYT  309 (539)
T ss_pred             HHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhH-HHHHHHHHHHHHHHHhh---------------hhhh
Confidence            8887753  3344445566677888877777666666665553 23344444555554433               5777


Q ss_pred             cCCChhHHHHHHHhcccC--ChhhHHHH--H----HHHHhc--CCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHh
Q 040338          244 EGGSTQKADLAFELMSRR--NMISWMVL--I----SAFSQA--GVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAK  313 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~~--~~~~~~~l--i----~~~~~~--g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  313 (385)
                      +.++.+.|+..|.+...+  +..+.+.+  .    ....+.  -+++.|.+.   -.-...+.+.|++..|...+.++++
T Consensus       310 k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~---r~kGne~Fk~gdy~~Av~~YteAIk  386 (539)
T KOG0548|consen  310 KREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEE---REKGNEAFKKGDYPEAVKHYTEAIK  386 (539)
T ss_pred             hHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHH---HHHHHHHHhccCHHHHHHHHHHHHh
Confidence            778999999999876542  21111111  0    000000  011111111   1225667789999999999999999


Q ss_pred             ccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          314 FTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       314 ~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..+  ...|.-..-+|.+.|.+..|++=.+...+.  +....|..=..++....++++|++.|++.++.+|..
T Consensus       387 r~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale~dp~~  459 (539)
T KOG0548|consen  387 RDPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALELDPSN  459 (539)
T ss_pred             cCCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchh
Confidence            988  888999999999999999998877666653  345567777777778889999999999999888654

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

Probab=97.99  E-value=0.00068  Score=55.66  Aligned_cols=114  Identities=11%  Similarity=0.024  Sum_probs=80.9

Q ss_pred             HHHHHhcCCCCchHHHH-------HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHH----HccCCHHHHHH
Q 040338          270 ISAFSQAGVLEKPRFFF-------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLL----GLSGLLGEAKK  338 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~-------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~----~~~g~~~~A~~  338 (385)
                      ...|+..|++++|++..       +...=+....+..+.+.|.+.++.|.+.....+.+.|..++    .-.+++.+|.-
T Consensus       115 a~i~~~~~~~deAl~~~~~~~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~qdAfy  194 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHLGENLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQDAFY  194 (299)
T ss_pred             hHHhhcCCChHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhhhHHH
Confidence            34577778888888777       33333344556677888888888888777744444444443    44567888888


Q ss_pred             HHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          339 LIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       339 ~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +|++|.++  |+..+.+....++...|++++|..++++.++..++.+
T Consensus       195 ifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dp  241 (299)
T KOG3081|consen  195 IFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDP  241 (299)
T ss_pred             HHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCH
Confidence            88888875  7788888888888888888888888888887766543

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=97.99  E-value=0.00085  Score=54.98  Aligned_cols=152  Identities=13%  Similarity=0.036  Sum_probs=121.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|+-+....+....... .+.|....+..+....+.|++.+|...|.+.....                   ++|-.+|+
T Consensus        79 ~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-------------------p~d~~~~~  138 (257)
T COG5010          79 RGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-------------------PTDWEAWN  138 (257)
T ss_pred             cccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-------------------CCChhhhh
Confidence            67777777776665443 23456677778899999999999999999987776                   58999999


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      .+--+|.+.|++++|..-|.+..+.  .| +...++.+...+.-.|+.+.|..++......+.                 
T Consensus       139 ~lgaaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~-----------------  199 (257)
T COG5010         139 LLGAALDQLGRFDEARRAYRQALEL--APNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPA-----------------  199 (257)
T ss_pred             HHHHHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCC-----------------
Confidence            9999999999999999999998874  55 456677888888888999999999998877653                 


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR  261 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  261 (385)
                            -|..+-+.+.......|+++.|..+-..-..+
T Consensus       200 ------ad~~v~~NLAl~~~~~g~~~~A~~i~~~e~~~  231 (257)
T COG5010         200 ------ADSRVRQNLALVVGLQGDFREAEDIAVQELLS  231 (257)
T ss_pred             ------CchHHHHHHHHHHhhcCChHHHHhhccccccc
Confidence                  24445578888889999999999887655443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.98  E-value=0.001  Score=64.21  Aligned_cols=132  Identities=5%  Similarity=-0.151  Sum_probs=107.8

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCC-CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVS-DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                      ++..+-.|-.....   .|+.++|..+++...+.  .| +......+...+.+.+++++|+..+++....+         
T Consensus        85 ~~~~~~~La~i~~~---~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~---------  150 (694)
T PRK15179         85 TELFQVLVARALEA---AHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG---------  150 (694)
T ss_pred             cHHHHHHHHHHHHH---cCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC---------
Confidence            35555666666555   89999999999999986  44 45667778899999999999999999988776         


Q ss_pred             HHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          127 RLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       127 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                                +.+....+.+-.++.+.|++++|..+|++.... .+-+..++..+-.++...|+.++|...|+...+.
T Consensus       151 ----------p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~-~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        151 ----------SSSAREILLEAKSWDEIGQSEQADACFERLSRQ-HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             ----------CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhc-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                      356677788888999999999999999999873 2224778888888899999999999999998876

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=97.97  E-value=0.002  Score=57.49  Aligned_cols=149  Identities=13%  Similarity=0.017  Sum_probs=102.2

Q ss_pred             CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHH
Q 040338          228 IESSIQIGKALVTMYAEGGSTQKADLAFELMSRR-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSG  294 (385)
Q Consensus       228 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~  294 (385)
                      ..|+...+...+.+......-..+-.++.+-.+| ...........+...|++++|+..+            .+....+.
T Consensus       270 d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~aa~YG~A~~~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i  349 (484)
T COG4783         270 DSPDFQLARARIRAKYEALPNQQAADLLAKRSKRGGLAAQYGRALQTYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDI  349 (484)
T ss_pred             CCccHHHHHHHHHHHhccccccchHHHHHHHhCccchHHHHHHHHHHHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            4555556666666555544444444443333332 2223333344455677788777777            55667777


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHH
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      +.+.++.++|.+.++++....+  ....-.+.++|.+.|++.+|++.+++....  .|...|..|.++|...|+..++..
T Consensus       350 ~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~  429 (484)
T COG4783         350 LLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALL  429 (484)
T ss_pred             HHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHH
Confidence            8888888999999999888877  666667888899999999999998887664  467789999999988888877777


Q ss_pred             HHHHHH
Q 040338          371 VMRNLL  376 (385)
Q Consensus       371 ~~~~~~  376 (385)
                      ...+..
T Consensus       430 A~AE~~  435 (484)
T COG4783         430 ARAEGY  435 (484)
T ss_pred             HHHHHH
Confidence            666553

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=97.96  E-value=0.0054  Score=52.41  Aligned_cols=259  Identities=10%  Similarity=-0.018  Sum_probs=178.3

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHH---HHHHhCCCchHHHHHHHHH
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMI---SILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li---~~~~~~~~~~~a~~~~~~m  166 (385)
                      .--+-..+.-.|++.+|+.-|....+                      .|+..|.++.   ..|...|+...|+.=+++.
T Consensus        41 hlElGk~lla~~Q~sDALt~yHaAve----------------------~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rV   98 (504)
T KOG0624|consen   41 HLELGKELLARGQLSDALTHYHAAVE----------------------GDPNNYQAIFRRATVYLAMGKSKAALQDLSRV   98 (504)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHc----------------------CCchhHHHHHHHHHHHhhhcCCccchhhHHHH
Confidence            33455566667777777777766543                      4444455443   5678889988888888888


Q ss_pred             HHCCCCCCHhhHH-HHHHHhcCccCccchhhHHHHHHHhCCCC--chHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHH
Q 040338          167 WNHGFGLSSMLYA-TAFSARASVYDLEWGPHLHSRVVHMEPSL--DVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA  243 (385)
Q Consensus       167 ~~~g~~p~~~t~~-~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~  243 (385)
                      .+  ++||-..-. .--..+.+.|.++.|..=|+..++.....  ....++.+...-          ........+..+.
T Consensus        99 le--lKpDF~~ARiQRg~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~----------e~~~l~~ql~s~~  166 (504)
T KOG0624|consen   99 LE--LKPDFMAARIQRGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQ----------EHWVLVQQLKSAS  166 (504)
T ss_pred             Hh--cCccHHHHHHHhchhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHH----------HHHHHHHHHHHHh
Confidence            76  477743322 12334678999999999999999876532  233343333221          1122234566677


Q ss_pred             cCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHH
Q 040338          244 EGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      -.|+...|+.....+.+   .|...|..=..+|...|.+..|+.-+            ++--+-..+-..|+.+.+....
T Consensus       167 ~~GD~~~ai~~i~~llEi~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~i  246 (504)
T KOG0624|consen  167 GSGDCQNAIEMITHLLEIQPWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEI  246 (504)
T ss_pred             cCCchhhHHHHHHHHHhcCcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHH
Confidence            78999999999998876   37788888888999999999888766            5555666677788888888888


Q ss_pred             HHHHhccc-----hhhHHHH---------HHHHHccCCHHHHHHHHHhCCCC-CCc-----chHHHHHHHHHhcCChHHH
Q 040338          309 TAMAKFTY-----TCYFVCM---------VDLLGLSGLLGEAKKLIDEMPSK-PTC-----VIWGALLGACCSHYNTKLA  368 (385)
Q Consensus       309 ~~~~~~~~-----~~~~~~l---------i~~~~~~g~~~~A~~~~~~m~~~-p~~-----~~~~~li~~~~~~g~~~~a  368 (385)
                      .+..+.++     -+.|-.+         .....+.++|.++.+..+...+. |..     ..+..+-.++...|++.+|
T Consensus       247 RECLKldpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eA  326 (504)
T KOG0624|consen  247 RECLKLDPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEA  326 (504)
T ss_pred             HHHHccCcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHH
Confidence            88888777     2222221         22345678888888888776653 542     2345566778889999999


Q ss_pred             HHHHHHHHhccccC
Q 040338          369 ELVMRNLLQLDVKV  382 (385)
Q Consensus       369 ~~~~~~~~~~~~~~  382 (385)
                      ++...+.++..+.+
T Consensus       327 iqqC~evL~~d~~d  340 (504)
T KOG0624|consen  327 IQQCKEVLDIDPDD  340 (504)
T ss_pred             HHHHHHHHhcCchH
Confidence            99999999888764

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=97.95  E-value=0.00033  Score=65.16  Aligned_cols=151  Identities=12%  Similarity=0.030  Sum_probs=108.3

Q ss_pred             hHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHH------HHHHHHhcccCChhhH
Q 040338          233 QIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFF------VSLLSGCSHSGPVTKG  304 (385)
Q Consensus       233 ~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~------~~l~~~~~~~~~~~~a  304 (385)
                      ..|..+|.+|...|+..+|..+...-.+  ||...|..+.+......-+++|.++.-+      ..+.......++++++
T Consensus       425 emw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~  504 (777)
T KOG1128|consen  425 EMWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEA  504 (777)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHH
Confidence            3566777788888888888887765443  5777787777777776667777777611      1111112336788888


Q ss_pred             HHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCC-cchHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          305 KHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       305 ~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      .+.|+.-.+.++  ..+|-.+..+..+.++++.|.+.|..-.. .|+ ...||.+-.+|.+.|+..+|...+++..+.+.
T Consensus       505 ~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~  584 (777)
T KOG1128|consen  505 DKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNY  584 (777)
T ss_pred             HHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCC
Confidence            888888777776  77777788888888888888888877665 354 45688888888888888888888888877765


Q ss_pred             cCC
Q 040338          381 KVF  383 (385)
Q Consensus       381 ~~~  383 (385)
                      .++
T Consensus       585 ~~w  587 (777)
T KOG1128|consen  585 QHW  587 (777)
T ss_pred             CCC
Confidence            554

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

Probab=97.95  E-value=9.7e-05  Score=66.25  Aligned_cols=126  Identities=6%  Similarity=-0.092  Sum_probs=99.2

Q ss_pred             ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHH
Q 040338           82 YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLC  161 (385)
Q Consensus        82 g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  161 (385)
                      +.+.+......+++.+....+++++..++-+......                ....-..|..++++.|.+.|..++++.
T Consensus        61 ~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~----------------~~~~~~~t~ha~vR~~l~~~~~~~~l~  124 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPN----------------CSYLLPSTHHALVRQCLELGAEDELLE  124 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcc----------------cccccCccHHHHHHHHHhcCCHHHHHH
Confidence            4455677788888888888888888888877654321                002234466799999999999999999


Q ss_pred             HHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          162 TFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       162 ~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      ++..=...|+-||.+||+.|+..+.+.|++..|.++..+|...+...+..++.--+.++.+.
T Consensus       125 ~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  125 LLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            99998899999999999999999999999999999999998887777777776666665555

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 [].

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.95  E-value=0.00076  Score=56.27  Aligned_cols=93  Identities=8%  Similarity=-0.143  Sum_probs=46.8

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      +++.+..+.+..++++|++++..-.+.+                   +.+......|..+|....++..|-..|+.+.. 
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~-------------------p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~q-   72 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERS-------------------PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQ-   72 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcC-------------------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence            4455555555555666665554443333                   23444455555555566666666666666544 


Q ss_pred             CCCCCHhhHHH-HHHHhcCccCccchhhHHHHHHH
Q 040338          170 GFGLSSMLYAT-AFSARASVYDLEWGPHLHSRVVH  203 (385)
Q Consensus       170 g~~p~~~t~~~-ll~~~~~~~~~~~a~~~~~~~~~  203 (385)
                       ..|...-|.. -...+.+.+.+.+|..+...|.+
T Consensus        73 -l~P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D  106 (459)
T KOG4340|consen   73 -LHPELEQYRLYQAQSLYKACIYADALRVAFLLLD  106 (459)
T ss_pred             -hChHHHHHHHHHHHHHHHhcccHHHHHHHHHhcC
Confidence             2444444432 22334444555555555555543

>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=97.93  E-value=0.0007  Score=60.56  Aligned_cols=125  Identities=14%  Similarity=0.052  Sum_probs=96.6

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      ...+|+..+...++++.|..+|+++.+.+                    |  ...-.++..+...++..+|.+++.+...
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~--------------------p--ev~~~LA~v~l~~~~E~~AI~ll~~aL~  228 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERD--------------------P--EVAVLLARVYLLMNEEVEAIRLLNEALK  228 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcC--------------------C--cHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            34556666667788999999998887544                    3  3455678888888888999999999886


Q ss_pred             CCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCCh
Q 040338          169 HGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGST  248 (385)
Q Consensus       169 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~  248 (385)
                      . .+-+......-...+.+.++.+.|.++.+++....+                       .+-.+|..|..+|.+.|++
T Consensus       229 ~-~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP-----------------------~~f~~W~~La~~Yi~~~d~  284 (395)
T PF09295_consen  229 E-NPQDSELLNLQAEFLLSKKKYELALEIAKKAVELSP-----------------------SEFETWYQLAECYIQLGDF  284 (395)
T ss_pred             h-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCc-----------------------hhHHHHHHHHHHHHhcCCH
Confidence            4 233566666677778899999999999999988642                       2335678888888899999


Q ss_pred             hHHHHHHHhcc
Q 040338          249 QKADLAFELMS  259 (385)
Q Consensus       249 ~~A~~~~~~m~  259 (385)
                      +.|+..++.++
T Consensus       285 e~ALlaLNs~P  295 (395)
T PF09295_consen  285 ENALLALNSCP  295 (395)
T ss_pred             HHHHHHHhcCc
Confidence            99999999887

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

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.90  E-value=9.7e-05  Score=54.56  Aligned_cols=96  Identities=11%  Similarity=-0.028  Sum_probs=79.2

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC----cchHHHHHH
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT----CVIWGALLG  357 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~----~~~~~~li~  357 (385)
                      +......+...|++++|...++.+....+     ...+..+...+.+.|++++|.+.|+.+... |+    ...+..+..
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~   84 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGM   84 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHH
Confidence            34556667788999999999999887655     345667899999999999999999988763 44    346778888


Q ss_pred             HHHhcCChHHHHHHHHHHHhccccCC
Q 040338          358 ACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       358 ~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ++...|+.++|...++++.+..|.+.
T Consensus        85 ~~~~~~~~~~A~~~~~~~~~~~p~~~  110 (119)
T TIGR02795        85 SLQELGDKEKAKATLQQVIKRYPGSS  110 (119)
T ss_pred             HHHHhCChHHHHHHHHHHHHHCcCCh
Confidence            99999999999999999999988764

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.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.90  E-value=0.025  Score=54.41  Aligned_cols=112  Identities=12%  Similarity=0.051  Sum_probs=78.8

Q ss_pred             cCCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHH
Q 040338            6 SLKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMAL   72 (385)
Q Consensus         6 ~~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~   72 (385)
                      .++++..|.+-.+.+.+..........          +.++|..+++...   ..|..|-..+-..|..   .++.++|.
T Consensus        21 d~~qfkkal~~~~kllkk~Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d---~~~~d~~~   97 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKKHPNALYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRD---LGKLDEAV   97 (932)
T ss_pred             hhHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHH---HhhhhHHH
Confidence            457788888888887776544333332          7888888888655   3356677777777666   88899999


Q ss_pred             HHHHHHHHhccCCCchHHHhHHHHHHhcCChh----HHHHHHHhccCCCccccc
Q 040338           73 HLHGLVKKFYFVSDESIAKSSIDMHVKCGAVD----YAESAFLRMLNPSLFCWK  122 (385)
Q Consensus        73 ~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~----~a~~~~~~m~~~~~~~~~  122 (385)
                      .+|+...+.  .|+......+..+|.|.+++.    .|.++++...+.-..-|+
T Consensus        98 ~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~pk~~yyfWs  149 (932)
T KOG2053|consen   98 HLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKNFPKRAYYFWS  149 (932)
T ss_pred             HHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHH
Confidence            999888865  566777777888888876554    467777777666555555

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

Probab=97.89  E-value=0.00011  Score=55.83  Aligned_cols=94  Identities=9%  Similarity=-0.025  Sum_probs=77.8

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCCh
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNT  365 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~  365 (385)
                      .+...+...|+.++|.+.++.+...++  ...+..+...+...|++++|...++.....  .+...+..+...|...|++
T Consensus        22 ~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~  101 (135)
T TIGR02552        22 ALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEP  101 (135)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCH
Confidence            444556667788888888998888766  778888999999999999999999987653  4566788888899999999


Q ss_pred             HHHHHHHHHHHhccccCC
Q 040338          366 KLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~~  383 (385)
                      ++|...+++..+.+|.+.
T Consensus       102 ~~A~~~~~~al~~~p~~~  119 (135)
T TIGR02552       102 ESALKALDLAIEICGENP  119 (135)
T ss_pred             HHHHHHHHHHHHhccccc
Confidence            999999999999887664

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

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.79  E-value=0.0023  Score=61.94  Aligned_cols=134  Identities=8%  Similarity=-0.087  Sum_probs=105.4

Q ss_pred             cCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHH
Q 040338           83 FVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCT  162 (385)
Q Consensus        83 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  162 (385)
                      .+.++..+..|.....+.|..++|..+++...+..                   +.+......+...+.+.+++++|+..
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~-------------------Pd~~~a~~~~a~~L~~~~~~eeA~~~  142 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRF-------------------PDSSEAFILMLRGVKRQQGIEAGRAE  142 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC-------------------CCcHHHHHHHHHHHHHhccHHHHHHH
Confidence            45568889999999999999999999999887655                   35667788899999999999999999


Q ss_pred             HHHHHHCCCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHH
Q 040338          163 FIELWNHGFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTM  241 (385)
Q Consensus       163 ~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~  241 (385)
                      +++....  .|+ ......+..++.+.|++++|..+|+++...+. -+..++                      ..+...
T Consensus       143 ~~~~l~~--~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p-~~~~~~----------------------~~~a~~  197 (694)
T PRK15179        143 IELYFSG--GSSSAREILLEAKSWDEIGQSEQADACFERLSRQHP-EFENGY----------------------VGWAQS  197 (694)
T ss_pred             HHHHhhc--CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCC-CcHHHH----------------------HHHHHH
Confidence            9999885  564 55667778889999999999999999998442 223444                      444555


Q ss_pred             HHcCCChhHHHHHHHhccc
Q 040338          242 YAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       242 ~~~~g~~~~A~~~~~~m~~  260 (385)
                      +-+.|+.++|...|+...+
T Consensus       198 l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        198 LTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            5566677777777776653

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.77  E-value=0.0007  Score=61.43  Aligned_cols=196  Identities=14%  Similarity=-0.013  Sum_probs=126.7

Q ss_pred             hcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHH
Q 040338          185 RASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------------IESSIQIGKALVTMYAEGGSTQKAD  252 (385)
Q Consensus       185 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~  252 (385)
                      +.+.|++.+|.-.|+..++..+ -+...|--|-......++-.            .+.+..+..+|.-.|...|.-..|.
T Consensus       295 lm~nG~L~~A~LafEAAVkqdP-~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~Al  373 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQDP-QHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQAL  373 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhCh-HHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHHH
Confidence            3466777788877877776643 22233322222222111111            3455677777888888888888888


Q ss_pred             HHHHhccc--C---------------------ChhhHHHHHHHHHhcCCCCch-HHHHHHHHHHHHhcccCChhhHHHHH
Q 040338          253 LAFELMSR--R---------------------NMISWMVLISAFSQAGVLEKP-RFFFFFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       253 ~~~~~m~~--~---------------------~~~~~~~li~~~~~~g~~~~a-~~~~~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      .++++-..  |                     +......+-..|....+-... ++-=....|.-.|--.|++++|...|
T Consensus       374 ~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf  453 (579)
T KOG1125|consen  374 KMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCF  453 (579)
T ss_pred             HHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHH
Confidence            88876642  0                     111122222222211111000 00005566666777889999999999


Q ss_pred             HHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCC-cchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          309 TAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       309 ~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      +.+....+  ...||-|...++...+.++|+..|++..+ +|+ ++..-.|.-+|...|.+++|...|=+.+.+..+
T Consensus       454 ~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq~k  530 (579)
T KOG1125|consen  454 EAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSMQRK  530 (579)
T ss_pred             HHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHhhhc
Confidence            99988888  88999999999999999999999999887 476 456667788889999999999888877765544

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=97.76  E-value=0.0025  Score=52.29  Aligned_cols=153  Identities=9%  Similarity=-0.058  Sum_probs=118.0

Q ss_pred             HhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCC
Q 040338           91 KSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHG  170 (385)
Q Consensus        91 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  170 (385)
                      ..+-..+.-.|+-+....+........                   +.|...-+.++....+.|++.+|+..+++.... 
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~-------------------~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-  129 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAY-------------------PKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL-  129 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccC-------------------cccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-
Confidence            455566666777777777765543322                   245556677889999999999999999999764 


Q ss_pred             CCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhH
Q 040338          171 FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQK  250 (385)
Q Consensus       171 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~  250 (385)
                      -++|..+|+.+--+|-+.|+.+.|..-|.+..+.-+.                       +....++|.-.|.-.|+.+.
T Consensus       130 ~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~-----------------------~p~~~nNlgms~~L~gd~~~  186 (257)
T COG5010         130 APTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPN-----------------------EPSIANNLGMSLLLRGDLED  186 (257)
T ss_pred             CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccC-----------------------CchhhhhHHHHHHHcCCHHH
Confidence            4568899999999999999999999999998886432                       22334677777777899999


Q ss_pred             HHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH
Q 040338          251 ADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF  286 (385)
Q Consensus       251 A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~  286 (385)
                      |..++.....   .|...-..+..+....|++++|..+-
T Consensus       187 A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         187 AETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhc
Confidence            9999987754   37777788888888899988887765

>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=97.76  E-value=0.0002  Score=49.99  Aligned_cols=93  Identities=14%  Similarity=0.036  Sum_probs=77.3

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g  363 (385)
                      +..+...+...|++++|...++.+.+..+  ...+..+...+...|++++|.+.++..... | +..++..+...+...|
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKLG   82 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHH
Confidence            44566677778999999999999887766  566777888899999999999999987653 3 4457888899999999


Q ss_pred             ChHHHHHHHHHHHhccc
Q 040338          364 NTKLAELVMRNLLQLDV  380 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~  380 (385)
                      ++++|...+++..+..|
T Consensus        83 ~~~~a~~~~~~~~~~~~   99 (100)
T cd00189          83 KYEEALEAYEKALELDP   99 (100)
T ss_pred             hHHHHHHHHHHHHccCC
Confidence            99999999999887765

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

Probab=97.76  E-value=0.00037  Score=62.61  Aligned_cols=120  Identities=12%  Similarity=-0.002  Sum_probs=99.4

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh--ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccch
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF--YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGI  125 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~--g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~  125 (385)
                      +......++..   +....+++.+..++-.....  ....-..|..++|+.|.+.|..+.++.+++.=..-|++      
T Consensus        65 S~~dld~fvn~---~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF------  135 (429)
T PF10037_consen   65 SSLDLDIFVNN---VESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIF------  135 (429)
T ss_pred             cHHHHHHHHhh---cCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccC------
Confidence            45556666776   44478889999999888876  33344566779999999999999999999888888884      


Q ss_pred             HHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCc
Q 040338          126 IRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASV  188 (385)
Q Consensus       126 ~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  188 (385)
                                  ||..++|.||+.+.+.|++..|.++..+|...+...+..|+...+.+|.+-
T Consensus       136 ------------~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  136 ------------PDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             ------------CChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence                        999999999999999999999999999999888888888888777777665

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=97.73  E-value=0.00061  Score=60.92  Aligned_cols=118  Identities=11%  Similarity=0.017  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHh
Q 040338          234 IGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAK  313 (385)
Q Consensus       234 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  313 (385)
                      .-.+|+..+...++++.|+.+|+++.+.+......++..+...++-.+|+++                      +.+..+
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~l----------------------l~~aL~  228 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRL----------------------LNEALK  228 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHH----------------------HHHHHH
Confidence            3355677777788999999999999987766666677777666655455444                      444333


Q ss_pred             ccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHHHHHhcCChHHHHHHHH
Q 040338          314 FTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLGACCSHYNTKLAELVMR  373 (385)
Q Consensus       314 ~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~  373 (385)
                      ..+  ...+..-.+.|.+.++++.|.++.+++.+. |+ ..+|..|..+|...|+++.|+..++
T Consensus       229 ~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLN  292 (395)
T PF09295_consen  229 ENPQDSELLNLQAEFLLSKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALN  292 (395)
T ss_pred             hCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence            333  333333344445555555555555555442 32 2255555555555555555554444

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

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.71  E-value=0.00073  Score=58.42  Aligned_cols=205  Identities=15%  Similarity=0.106  Sum_probs=101.7

Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHC----CCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNH----GFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      |.-....|-..+++++|.+.|.+..+.    +-..+ ...|.....++.+ .++++|.+.+++...              
T Consensus        38 y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~-~~~~~Ai~~~~~A~~--------------  102 (282)
T PF14938_consen   38 YEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKK-GDPDEAIECYEKAIE--------------  102 (282)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHH--------------
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh-hCHHHHHHHHHHHHH--------------
Confidence            444566777788888888888776432    11111 1223333333322 255555555544432              


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcC-CChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhc
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEG-GSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCS  296 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~-g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~  296 (385)
                       .|.+.|++.  .-...+..+...|-+. |++++|++.|++..           ..|...|....+.+  ++..+...+.
T Consensus       103 -~y~~~G~~~--~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~-----------~~y~~e~~~~~a~~--~~~~~A~l~~  166 (282)
T PF14938_consen  103 -IYREAGRFS--QAAKCLKELAEIYEEQLGDYEKAIEYYQKAA-----------ELYEQEGSPHSAAE--CLLKAADLYA  166 (282)
T ss_dssp             -HHHHCT-HH--HHHHHHHHHHHHHCCTT--HHHHHHHHHHHH-----------HHHHHTT-HHHHHH--HHHHHHHHHH
T ss_pred             -HHHhcCcHH--HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----------HHHHHCCChhhHHH--HHHHHHHHHH
Confidence             223322110  0112334444555555 56666655555443           22222221111111  4556667777


Q ss_pred             ccCChhhHHHHHHHHHhccc---------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC------cchHHHHHHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFTY---------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT------CVIWGALLGACC  360 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~---------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~------~~~~~~li~~~~  360 (385)
                      +.|++++|..+|+++.....         ...+...+-++...|++-.|.+.|++.... |.      ......|+.+|-
T Consensus       167 ~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~  246 (282)
T PF14938_consen  167 RLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYE  246 (282)
T ss_dssp             HTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHH
Confidence            88888888888888776433         223333444666688899999999887653 32      224555677765


Q ss_pred             hc--CChHHHHHHHHHHHhc
Q 040338          361 SH--YNTKLAELVMRNLLQL  378 (385)
Q Consensus       361 ~~--g~~~~a~~~~~~~~~~  378 (385)
                      ..  ..++.++.-|+.+.++
T Consensus       247 ~~D~e~f~~av~~~d~~~~l  266 (282)
T PF14938_consen  247 EGDVEAFTEAVAEYDSISRL  266 (282)
T ss_dssp             TT-CCCHHHHCHHHTTSS--
T ss_pred             hCCHHHHHHHHHHHcccCcc
Confidence            42  2344555555554443

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

Probab=97.68  E-value=0.00031  Score=49.68  Aligned_cols=81  Identities=5%  Similarity=0.094  Sum_probs=66.8

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCC--------CchHHHH
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHG--------FGFETLC  161 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~--------~~~~a~~  161 (385)
                      ...-|.-+...+++...-.+|+.+++.|+.                 -|++.+||.++.+.++..        +.-..+.
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~-----------------lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLt   90 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGIT-----------------LPSVELYNKVLKSIAKRELDSEDIENKLTNLLT   90 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCC-----------------CCcHHHHHHHHHHHHHccccchhHHHHHHHHHH
Confidence            344566666779999999999999988862                 599999999999887653        2345788


Q ss_pred             HHHHHHHCCCCCCHhhHHHHHHHhcC
Q 040338          162 TFIELWNHGFGLSSMLYATAFSARAS  187 (385)
Q Consensus       162 ~~~~m~~~g~~p~~~t~~~ll~~~~~  187 (385)
                      +|+.|...+++|+..||+.++..+.+
T Consensus        91 vYqDiL~~~lKP~~etYnivl~~Llk  116 (120)
T PF08579_consen   91 VYQDILSNKLKPNDETYNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHhccCCcHHHHHHHHHHHHH
Confidence            99999999999999999999987754

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 [, , ].

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=97.68  E-value=0.011  Score=57.41  Aligned_cols=147  Identities=12%  Similarity=-0.006  Sum_probs=99.3

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc---cccc----
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL---FCWK----  122 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~~~~----  122 (385)
                      ..|..|-.-|+.   ..+..+|.+.|+..-+.. ..+......+.+.|++..+++.|..+.-...+...   ..|+    
T Consensus       493 paf~~LG~iYrd---~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~r  568 (1238)
T KOG1127|consen  493 PAFAFLGQIYRD---SDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQR  568 (1238)
T ss_pred             HHHHHHHHHHHH---HHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhc
Confidence            356666666555   457888888888887654 33677888899999999999999998655433221   1111    


Q ss_pred             -------cchHHHHHHhcCC---CCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHH--HhcCccC
Q 040338          123 -------FGIIRLLIMFQKM---PERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS--ARASVYD  190 (385)
Q Consensus       123 -------~~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~--~~~~~~~  190 (385)
                             ++...|..-|+.-   .+.|...|..|..+|.+.|++..|+++|++...  +.|+. +|.....  .-+..|.
T Consensus       569 G~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~--LrP~s-~y~~fk~A~~ecd~Gk  645 (1238)
T KOG1127|consen  569 GPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASL--LRPLS-KYGRFKEAVMECDNGK  645 (1238)
T ss_pred             cccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHh--cCcHh-HHHHHHHHHHHHHhhh
Confidence                   6666666555443   345788899999999999999999999998865  45533 3322221  2345566


Q ss_pred             ccchhhHHHHHHH
Q 040338          191 LEWGPHLHSRVVH  203 (385)
Q Consensus       191 ~~~a~~~~~~~~~  203 (385)
                      +.++...++....
T Consensus       646 Ykeald~l~~ii~  658 (1238)
T KOG1127|consen  646 YKEALDALGLIIY  658 (1238)
T ss_pred             HHHHHHHHHHHHH
Confidence            7777666665553

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.64  E-value=0.023  Score=46.60  Aligned_cols=186  Identities=13%  Similarity=0.092  Sum_probs=127.7

Q ss_pred             hhhhHHHHHhhhC--------CCCh-hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCCh
Q 040338           33 LIDDDYRVFCDIG--------PRYL-FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAV  103 (385)
Q Consensus        33 ~~~~A~~~~~~~~--------~~~~-~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~  103 (385)
                      +.++..+++..+.        .++. ..|..++-+.   ...|+...|...++.+... ++-+..+-..=.-.+-..|++
T Consensus        27 nseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAA---ld~~~~~lAq~C~~~L~~~-fp~S~RV~~lkam~lEa~~~~  102 (289)
T KOG3060|consen   27 NSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAA---LDTGRDDLAQKCINQLRDR-FPGSKRVGKLKAMLLEATGNY  102 (289)
T ss_pred             CHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHH---HHhcchHHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhch
Confidence            7777777777665        1222 2344444443   3379999999999998876 333333322222334447999


Q ss_pred             hHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040338          104 DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS  183 (385)
Q Consensus       104 ~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  183 (385)
                      ++|.++++.+.+.+                   +.|.++|..=+...-..|+..+|++-+.+..+. +..|...|.-+..
T Consensus       103 ~~A~e~y~~lL~dd-------------------pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLae  162 (289)
T KOG3060|consen  103 KEAIEYYESLLEDD-------------------PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAE  162 (289)
T ss_pred             hhHHHHHHHHhccC-------------------cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHH
Confidence            99999999998887                   478888888777777888888999888888776 6779999999999


Q ss_pred             HhcCccCccchhhHHHHHHHhCCCCchHHH-HHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCC
Q 040338          184 ARASVYDLEWGPHLHSRVVHMEPSLDVFVG-SGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRN  262 (385)
Q Consensus       184 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~  262 (385)
                      .|...|++++|.-.+++++=..  |....| ..+.+.+.-.|                   -..+++-|.+.|..-.+-+
T Consensus       163 iY~~~~~f~kA~fClEE~ll~~--P~n~l~f~rlae~~Yt~g-------------------g~eN~~~arkyy~~alkl~  221 (289)
T KOG3060|consen  163 IYLSEGDFEKAAFCLEELLLIQ--PFNPLYFQRLAEVLYTQG-------------------GAENLELARKYYERALKLN  221 (289)
T ss_pred             HHHhHhHHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHHh-------------------hHHHHHHHHHHHHHHHHhC
Confidence            9999999999999999998653  333332 22222221111                   1235677888887777644


Q ss_pred             h
Q 040338          263 M  263 (385)
Q Consensus       263 ~  263 (385)
                      .
T Consensus       222 ~  222 (289)
T KOG3060|consen  222 P  222 (289)
T ss_pred             h
Confidence            3

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.60  E-value=0.046  Score=49.83  Aligned_cols=113  Identities=13%  Similarity=0.098  Sum_probs=72.3

Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhccc----C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSR----R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSG  294 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~  294 (385)
                      ..+|...++.-.+..-++.|..+|.+..+    + ++..++++++-||. ++..-|.++|            -....++-
T Consensus       366 tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~d~p~yv~~Yldf  444 (656)
T KOG1914|consen  366 TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFGDSPEYVLKYLDF  444 (656)
T ss_pred             ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence            34567777777788889999999998876    2 66777788877764 3445555555            22334444


Q ss_pred             hcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      +.+.++-..+..+|++......     ..+|..+++--..-|++..+.++-+++..
T Consensus       445 L~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  445 LSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            4555555666666666665533     45666666666666666666666655554

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.57  E-value=0.0026  Score=48.90  Aligned_cols=123  Identities=10%  Similarity=0.036  Sum_probs=76.1

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC--CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHGFGL--SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDM  219 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  219 (385)
                      .|..++..+ ..++...+...++.+.+....-  .....-.+...+...|++++|...|+........|+..        
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~--------   84 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELK--------   84 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHH--------
Confidence            455556565 4778888888888887752111  12333345566778889999999998888876322211        


Q ss_pred             HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC--ChhhHHHHHHHHHhcCCCCchHHH
Q 040338          220 YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR--NMISWMVLISAFSQAGVLEKPRFF  285 (385)
Q Consensus       220 ~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~li~~~~~~g~~~~a~~~  285 (385)
                                  ....-.+...+...|++++|+..++....+  ....+......|.+.|+.++|...
T Consensus        85 ------------~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~  140 (145)
T PF09976_consen   85 ------------PLARLRLARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAA  140 (145)
T ss_pred             ------------HHHHHHHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHH
Confidence                        112244667777888888998888775443  223344445556666666555544

>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=97.56  E-value=0.00052  Score=47.74  Aligned_cols=97  Identities=11%  Similarity=0.014  Sum_probs=76.5

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      ++..+...+...|++++|...+++..+..                   +.+...+..+...+...+++++|.+.++....
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~   62 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-------------------PDNADAYYNLAAAYYKLGKYEEALEDYEKALE   62 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-------------------CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35567778888999999999998876554                   24446777888889999999999999999877


Q ss_pred             CCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          169 HGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       169 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      .. +.+..++..+...+...|+.+.|...+....+..
T Consensus        63 ~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~   98 (100)
T cd00189          63 LD-PDNAKAYYNLGLAYYKLGKYEEALEAYEKALELD   98 (100)
T ss_pred             CC-CcchhHHHHHHHHHHHHHhHHHHHHHHHHHHccC
Confidence            53 3344677788888899999999999988876543

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=97.54  E-value=0.02  Score=55.82  Aligned_cols=170  Identities=12%  Similarity=-0.018  Sum_probs=108.4

Q ss_pred             CChHHHHHHHHHHHHhccCCC-chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           66 GNIKMALHLHGLVKKFYFVSD-ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .+...++..|-...+.  .|+ ...|..|...|+..-+...|.+.|+..-+.+                   ..+...+.
T Consensus       472 K~~~~al~ali~alrl--d~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-------------------atdaeaaa  530 (1238)
T KOG1127|consen  472 KNSALALHALIRALRL--DVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD-------------------ATDAEAAA  530 (1238)
T ss_pred             hhHHHHHHHHHHHHhc--ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-------------------chhhhhHH
Confidence            5566666666555543  333 4678999999999889999999998877665                   46777888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHH--HhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFS--ARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYL  221 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  221 (385)
                      .....|++...++.|..+.-.--+  ..| -...++.+-+  .+.+.++...++.-|+...+..+ -|...|..+..+|.
T Consensus       531 a~adtyae~~~we~a~~I~l~~~q--ka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dP-kD~n~W~gLGeAY~  607 (1238)
T KOG1127|consen  531 ASADTYAEESTWEEAFEICLRAAQ--KAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDP-KDYNLWLGLGEAYP  607 (1238)
T ss_pred             HHHHHhhccccHHHHHHHHHHHhh--hchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCc-hhHHHHHHHHHHHH
Confidence            888999999999999888333222  122 2223333322  35677888888888888776643 45666667777777


Q ss_pred             hcCCCC-----------CCchh-hHHHHHHHHHHcCCChhHHHHHHHhcc
Q 040338          222 KCGCNG-----------IESSI-QIGKALVTMYAEGGSTQKADLAFELMS  259 (385)
Q Consensus       222 ~~g~~~-----------~~~~~-~~~~~li~~~~~~g~~~~A~~~~~~m~  259 (385)
                      ++|...           ..|+. ..--......+..|.+.+|...+..+.
T Consensus       608 ~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  608 ESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             hcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            766555           22221 111122233345567777777766654

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

Probab=97.53  E-value=0.00018  Score=49.46  Aligned_cols=81  Identities=11%  Similarity=0.023  Sum_probs=60.5

Q ss_pred             cCChHHHHHHHHHHHHhccC-CCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           65 VGNIKMALHLHGLVKKFYFV-SDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      .|+++.|+.+++++.+.... ++...+-.+..+|.+.|++++|..++++ .+.+                   +.+....
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~-------------------~~~~~~~   61 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD-------------------PSNPDIH   61 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH-------------------HCHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC-------------------CCCHHHH
Confidence            58899999999999987542 2455566688999999999999999988 3222                   1333444


Q ss_pred             HHHHHHHHhCCCchHHHHHHHH
Q 040338          144 NTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      -.+..++.+.|++++|+++|++
T Consensus        62 ~l~a~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   62 YLLARCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHhc
Confidence            4567889999999999999875

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

Probab=97.51  E-value=0.015  Score=48.12  Aligned_cols=50  Identities=12%  Similarity=0.010  Sum_probs=27.6

Q ss_pred             CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          154 GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       154 ~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      ++..+|.-+|++|.++ ..|+..+.+-...++...|++++|..+++..+..
T Consensus       187 ek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  187 EKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             hhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            4455555555555443 4555555555555555555555555555555554

>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=97.50  E-value=0.00075  Score=53.95  Aligned_cols=88  Identities=10%  Similarity=0.082  Sum_probs=71.7

Q ss_pred             CCCcchHHHHHHHHHhC-----CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc----------------Cccchh
Q 040338          137 ERDLVSWNTMISILTRH-----GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY----------------DLEWGP  195 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~----------------~~~~a~  195 (385)
                      ..|-.+|..++..|.+.     |..+=....+..|.+.|+.-|..+|+.|++.+=+..                +-+-|+
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i  123 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAI  123 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHH
Confidence            56778888888888754     677778889999999999999999999999876532                356788


Q ss_pred             hHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          196 HLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      +++++|...|+-||..++..|++.+++.+
T Consensus       124 ~lL~qME~~gV~Pd~Et~~~ll~iFG~~s  152 (228)
T PF06239_consen  124 DLLEQMENNGVMPDKETEQMLLNIFGRKS  152 (228)
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhcccc
Confidence            99999999999888888877777776554

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

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.47  E-value=0.0016  Score=47.89  Aligned_cols=103  Identities=12%  Similarity=-0.052  Sum_probs=76.6

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      .++..+...+.+.|++++|.+.|+++.+....                .......+..+..++.+.|++++|...|+.+.
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~----------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~   66 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPK----------------STYAPNAHYWLGEAYYAQGKYADAAKAFLAVV   66 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC----------------ccccHHHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence            45667778888899999999999888654320                01123456668888999999999999999987


Q ss_pred             HCCCC--CCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          168 NHGFG--LSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       168 ~~g~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      .....  .....+..+..++.+.|+.++|.+.++++.+..+
T Consensus        67 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p  107 (119)
T TIGR02795        67 KKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKRYP  107 (119)
T ss_pred             HHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHHCc
Confidence            64211  1244566777788889999999999999988854

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.

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.42  E-value=0.00025  Score=45.94  Aligned_cols=60  Identities=18%  Similarity=0.097  Sum_probs=49.3

Q ss_pred             HHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          323 MVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       323 li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +...+.+.|++++|.+.|++..+. | +...+..+..++...|++++|...++++++..|.+
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~   64 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPDN   64 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence            456788899999999999998875 5 55678888899999999999999999999888765

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.41  E-value=0.0083  Score=56.03  Aligned_cols=244  Identities=10%  Similarity=0.044  Sum_probs=123.1

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh-ccCC--------CchHHHhHHHHHHhcCCh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF-YFVS--------DESIAKSSIDMHVKCGAV  103 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-g~~~--------~~~~~~~li~~~~~~g~~  103 (385)
                      .+++|.++.+.  .|.+..|..+......   .-.++.|...|-..... |++.        +.+.-.+=|.+|  -|++
T Consensus       678 gledA~qfiEd--nPHprLWrllAe~Al~---Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~f  750 (1189)
T KOG2041|consen  678 GLEDAIQFIED--NPHPRLWRLLAEYALF---KLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEF  750 (1189)
T ss_pred             chHHHHHHHhc--CCchHHHHHHHHHHHH---HHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcch
Confidence            45555555554  4556667766555333   56666676666555432 2211        011111111222  3556


Q ss_pred             hHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC----CHhhHH
Q 040338          104 DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL----SSMLYA  179 (385)
Q Consensus       104 ~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p----~~~t~~  179 (385)
                      ++|+++|-+|-.++.                           .|..+.+.|+|-.+.++++.-   |-..    -...++
T Consensus       751 eeaek~yld~drrDL---------------------------Aielr~klgDwfrV~qL~r~g---~~d~dD~~~e~A~r  800 (1189)
T KOG2041|consen  751 EEAEKLYLDADRRDL---------------------------AIELRKKLGDWFRVYQLIRNG---GSDDDDEGKEDAFR  800 (1189)
T ss_pred             hHhhhhhhccchhhh---------------------------hHHHHHhhhhHHHHHHHHHcc---CCCcchHHHHHHHH
Confidence            666666544433332                           455666667776655555321   1111    123455


Q ss_pred             HHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcc
Q 040338          180 TAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMS  259 (385)
Q Consensus       180 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  259 (385)
                      .+-..+.....+++|.+.+..-...                               ...+.++.+..++++-+.+-..++
T Consensus       801 ~ig~~fa~~~~We~A~~yY~~~~~~-------------------------------e~~~ecly~le~f~~LE~la~~Lp  849 (1189)
T KOG2041|consen  801 NIGETFAEMMEWEEAAKYYSYCGDT-------------------------------ENQIECLYRLELFGELEVLARTLP  849 (1189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccch-------------------------------HhHHHHHHHHHhhhhHHHHHHhcC
Confidence            5555555555666666555543211                               233444444445555544444444


Q ss_pred             cCChhhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHHhccc-------------hhhHHH
Q 040338          260 RRNMISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-------------TCYFVC  322 (385)
Q Consensus       260 ~~~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------------~~~~~~  322 (385)
                      + |....-.+.+.+.+.|.-++|.+.+    .-...+.+|...++|.+|.++-+...-...             ..-..-
T Consensus       850 e-~s~llp~~a~mf~svGMC~qAV~a~Lr~s~pkaAv~tCv~LnQW~~avelaq~~~l~qv~tliak~aaqll~~~~~~e  928 (1189)
T KOG2041|consen  850 E-DSELLPVMADMFTSVGMCDQAVEAYLRRSLPKAAVHTCVELNQWGEAVELAQRFQLPQVQTLIAKQAAQLLADANHME  928 (1189)
T ss_pred             c-ccchHHHHHHHHHhhchHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHhhcchHH
Confidence            2 3333444555555555555555544    222345666677777776666554322111             111112


Q ss_pred             HHHHHHccCCHHHHHHHHHhCCC
Q 040338          323 MVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       323 li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      -|..+.++|+.-+|-+++.+|.+
T Consensus       929 aIe~~Rka~~~~daarll~qmae  951 (1189)
T KOG2041|consen  929 AIEKDRKAGRHLDAARLLSQMAE  951 (1189)
T ss_pred             HHHHhhhcccchhHHHHHHHHhH
Confidence            36667788888888888888866

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.41  E-value=0.0031  Score=54.52  Aligned_cols=114  Identities=15%  Similarity=0.145  Sum_probs=76.6

Q ss_pred             HHHHHHHHHhcCCCCchHHHHHHHHHHHHhccc-CChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHH
Q 040338          266 WMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHS-GPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEA  336 (385)
Q Consensus       266 ~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A  336 (385)
                      |...+..|...|++..|-.  .+..+...|-.. |+++.|.+.|++......        ...+..+...+.+.|++++|
T Consensus        97 ~~~A~~~y~~~G~~~~aA~--~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A  174 (282)
T PF14938_consen   97 YEKAIEIYREAGRFSQAAK--CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEA  174 (282)
T ss_dssp             HHHHHHHHHHCT-HHHHHH--HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             HHHHHHHHHhcCcHHHHHH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHH
Confidence            3333444444444444332  567888888888 999999999998877533        66677788899999999999


Q ss_pred             HHHHHhCCCC----C----Ccc-hHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          337 KKLIDEMPSK----P----TCV-IWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       337 ~~~~~~m~~~----p----~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      .++|+++...    +    +.. .|-..+-++...||...|.+.+++..+..|.
T Consensus       175 ~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~  228 (282)
T PF14938_consen  175 IEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPS  228 (282)
T ss_dssp             HHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTT
T ss_pred             HHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            9999987542    2    111 2233344566679999999999999877653

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.40  E-value=0.032  Score=50.77  Aligned_cols=175  Identities=10%  Similarity=-0.041  Sum_probs=125.3

Q ss_pred             hHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC-CcchHHHH
Q 040338           68 IKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER-DLVSWNTM  146 (385)
Q Consensus        68 ~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l  146 (385)
                      .+.....++.+...-..--..+|..+|+.-.+..-++.|..+|.+..+...                  .+ ++.+++++
T Consensus       347 ~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r------------------~~hhVfVa~A~  408 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKR------------------TRHHVFVAAAL  408 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccC------------------CcchhhHHHHH
Confidence            445555666665542222345688889999999999999999999877654                  34 78899999


Q ss_pred             HHHHHhCCCchHHHHHHHHHHHCCCCCCHhhH-HHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 040338          147 ISILTRHGFGFETLCTFIELWNHGFGLSSMLY-ATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGC  225 (385)
Q Consensus       147 i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  225 (385)
                      |..|| .++.+-|.++|+.-.+.  -+|...| ..-+..++..++-..+..+|+..+..++.|+.               
T Consensus       409 mEy~c-skD~~~AfrIFeLGLkk--f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~k---------------  470 (656)
T KOG1914|consen  409 MEYYC-SKDKETAFRIFELGLKK--FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADK---------------  470 (656)
T ss_pred             HHHHh-cCChhHHHHHHHHHHHh--cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhh---------------
Confidence            99888 56788999999886554  3454444 35677788899999999999999998776654               


Q ss_pred             CCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-------CChhhHHHHHHHHHhcCCCCchH
Q 040338          226 NGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-------RNMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       226 ~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~~~~~~~~li~~~~~~g~~~~a~  283 (385)
                           ...+|..+|.--..-|++..+.++-+.+..       +....-..+++-|.-.+....-.
T Consensus       471 -----s~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~~~c~~  530 (656)
T KOG1914|consen  471 -----SKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDLYPCSL  530 (656)
T ss_pred             -----hHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhcccccccH
Confidence                 335678888888888899988888776643       22234445566666555554433

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

Probab=97.39  E-value=0.0026  Score=54.80  Aligned_cols=131  Identities=12%  Similarity=0.127  Sum_probs=96.9

Q ss_pred             hHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHH
Q 040338          233 QIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMA  312 (385)
Q Consensus       233 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  312 (385)
                      .+|-.+++..-+.+.++.|..+|.+..+.+..+|...+.                 .++++ +...++.+.|..+|+...
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~-----------------~A~~E-~~~~~d~~~A~~Ife~gl   63 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVA-----------------YALME-YYCNKDPKRARKIFERGL   63 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHH-----------------HHHHH-HHTCS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHH-----------------HHHHH-HHhCCCHHHHHHHHHHHH
Confidence            356677777777778999999999988644434333221                 11221 122456677999999988


Q ss_pred             hccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCc----chHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          313 KFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTC----VIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       313 ~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      +...  ...+...++.+.+.|+.+.|..+|++.... |..    ..|...+..-.+.|+.+.+..+.+++.+.-+.
T Consensus        64 k~f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~  139 (280)
T PF05843_consen   64 KKFPSDPDFWLEYLDFLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPE  139 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT
T ss_pred             HHCCCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhh
Confidence            8777  788899999999999999999999999886 433    48999999999999999999999998876443

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.

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.38  E-value=0.083  Score=46.28  Aligned_cols=98  Identities=13%  Similarity=0.028  Sum_probs=72.8

Q ss_pred             hHHHHHHHHHhcCCCCchHHHH---------HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHH
Q 040338          265 SWMVLISAFSQAGVLEKPRFFF---------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGE  335 (385)
Q Consensus       265 ~~~~li~~~~~~g~~~~a~~~~---------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  335 (385)
                      +.+..|.-+...|+...|.++-         .|-..+.+++..++|++..++-..   ...+.-|..+++.+.+.|+..+
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s---kKsPIGyepFv~~~~~~~~~~e  255 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS---KKSPIGYEPFVEACLKYGNKKE  255 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC---CCCCCChHHHHHHHHHCCCHHH
Confidence            4555677777888888887777         788888999999999887776443   2237778888899999999999


Q ss_pred             HHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHH
Q 040338          336 AKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       336 A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      |.+++..+..       ..-+..|.+.|++.+|.+..
T Consensus       256 A~~yI~k~~~-------~~rv~~y~~~~~~~~A~~~A  285 (319)
T PF04840_consen  256 ASKYIPKIPD-------EERVEMYLKCGDYKEAAQEA  285 (319)
T ss_pred             HHHHHHhCCh-------HHHHHHHHHCCCHHHHHHHH
Confidence            9998877442       45566667777776665553

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

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.35  E-value=0.0012  Score=58.98  Aligned_cols=91  Identities=10%  Similarity=-0.050  Sum_probs=70.1

Q ss_pred             HHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHH
Q 040338          293 SGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLA  368 (385)
Q Consensus       293 ~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a  368 (385)
                      ..+...|+++.|++.|+++.+..+  ...+..+..+|.+.|++++|+..+++.... | +...|..+..+|...|++++|
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~eA   89 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTA   89 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCHHHH
Confidence            344567788888888888887777  667777788888888888888888887653 3 455777788888888888888


Q ss_pred             HHHHHHHHhccccCC
Q 040338          369 ELVMRNLLQLDVKVF  383 (385)
Q Consensus       369 ~~~~~~~~~~~~~~~  383 (385)
                      ...+++.++.+|.++
T Consensus        90 ~~~~~~al~l~P~~~  104 (356)
T PLN03088         90 KAALEKGASLAPGDS  104 (356)
T ss_pred             HHHHHHHHHhCCCCH
Confidence            888888888777653

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

Probab=97.35  E-value=0.00065  Score=46.67  Aligned_cols=77  Identities=14%  Similarity=0.150  Sum_probs=60.0

Q ss_pred             cCChhhHHHHHHHHHhccc----hhhHHHHHHHHHccCCHHHHHHHHHhCCCCC-CcchHHHHHHHHHhcCChHHHHHHH
Q 040338          298 SGPVTKGKHYFTAMAKFTY----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKP-TCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       298 ~~~~~~a~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p-~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      .|+++.|+.+++++.+..+    ...+..+..+|.+.|++++|..+++.....| +....-.+..+|.+.|++++|++.+
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l   81 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKAL   81 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            5789999999999998877    2344457899999999999999999832223 3345556688999999999999999


Q ss_pred             HH
Q 040338          373 RN  374 (385)
Q Consensus       373 ~~  374 (385)
                      ++
T Consensus        82 ~~   83 (84)
T PF12895_consen   82 EK   83 (84)
T ss_dssp             HH
T ss_pred             hc
Confidence            86

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.35  E-value=0.019  Score=47.13  Aligned_cols=173  Identities=13%  Similarity=0.078  Sum_probs=124.9

Q ss_pred             CCChHHHHHHHHHHHHc---c-cchhhHHh------------hhhhHHHHHhhhC--CCCh---h-hHHHHHHHHHhhhc
Q 040338            7 LKSLPIARKIHAQLIST---C-LISSIFLQ------------LIDDDYRVFCDIG--PRYL---F-TYNTMINGGVRCLC   64 (385)
Q Consensus         7 ~~~~~~a~~~~~~~~~~---~-~~~~~~~~------------~~~~A~~~~~~~~--~~~~---~-~~~~li~~~~~~~~   64 (385)
                      .++.++..+++.++...   | ..++.|+-            +.+.|...++.+.  -|++   . .+..++.+      
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa------   98 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEA------   98 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHH------
Confidence            35667777777777633   3 66676664            8888888888765  2332   2 22233333      


Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|+.++|.++++.+.+.. +.|..++.-=+-..-..|+-.+|++-+....+.-                   ..|...|.
T Consensus        99 ~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F-------------------~~D~EAW~  158 (289)
T KOG3060|consen   99 TGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKF-------------------MNDQEAWH  158 (289)
T ss_pred             hhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHh-------------------cCcHHHHH
Confidence            799999999999999986 5577788777777777788888888776665444                   47899999


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCH-hhHHHHHHHhcCc---cCccchhhHHHHHHHhCCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSS-MLYATAFSARASV---YDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~ll~~~~~~---~~~~~a~~~~~~~~~~~~~  207 (385)
                      -|-..|...|++++|.-.++++.-.  .|.. .-|..+...+...   .+.+.+.+.|...++....
T Consensus       159 eLaeiY~~~~~f~kA~fClEE~ll~--~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~~  223 (289)
T KOG3060|consen  159 ELAEIYLSEGDFEKAAFCLEELLLI--QPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNPK  223 (289)
T ss_pred             HHHHHHHhHhHHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhChH
Confidence            9999999999999999999999874  6644 4444555554433   4567788889888887653

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.30  E-value=0.063  Score=51.85  Aligned_cols=102  Identities=16%  Similarity=0.113  Sum_probs=71.6

Q ss_pred             hcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHH--HhCCCchHHHHHHHHHHHCCCCCCHh
Q 040338           99 KCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISIL--TRHGFGFETLCTFIELWNHGFGLSSM  176 (385)
Q Consensus        99 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~--~~~~~~~~a~~~~~~m~~~g~~p~~~  176 (385)
                      ..+++..|.+-.+++.++                    .||. .|...+.++  .+.|+.++|..+++.....+.. |..
T Consensus        21 d~~qfkkal~~~~kllkk--------------------~Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~   78 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKK--------------------HPNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDL   78 (932)
T ss_pred             hhHHHHHHHHHHHHHHHH--------------------CCCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chH
Confidence            346666776666665443                    2443 344555544  6889999999999888765444 888


Q ss_pred             hHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          177 LYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       177 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      |...+-.+|.+.++.++|..+|++..+..+  +......+..+|.|.+
T Consensus        79 tLq~l~~~y~d~~~~d~~~~~Ye~~~~~~P--~eell~~lFmayvR~~  124 (932)
T KOG2053|consen   79 TLQFLQNVYRDLGKLDEAVHLYERANQKYP--SEELLYHLFMAYVREK  124 (932)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHhhCC--cHHHHHHHHHHHHHHH
Confidence            999999999999999999999999987653  3554444555554433

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.30  E-value=0.0049  Score=55.18  Aligned_cols=98  Identities=5%  Similarity=-0.052  Sum_probs=79.9

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|+++.|+..+++.++.. +-+...|..+..+|.+.|++++|+..+++..+.+                   +.+...|.
T Consensus        15 ~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-------------------P~~~~a~~   74 (356)
T PLN03088         15 DDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-------------------PSLAKAYL   74 (356)
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------cCCHHHHH
Confidence            799999999999999875 3367788888899999999999999998887665                   35677888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSA  184 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  184 (385)
                      .+..+|...|++++|+..|++..+.  .|+......++..
T Consensus        75 ~lg~~~~~lg~~~eA~~~~~~al~l--~P~~~~~~~~l~~  112 (356)
T PLN03088         75 RKGTACMKLEEYQTAKAALEKGASL--APGDSRFTKLIKE  112 (356)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            8999999999999999999999874  5655554444433

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.22  E-value=0.0082  Score=47.67  Aligned_cols=125  Identities=14%  Similarity=0.035  Sum_probs=84.6

Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC--HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS--SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      ....+..+...+...|++++|...|++..+.+..+.  ...+..+...+.+.|++++|...+++..+..+. +...+..+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l  112 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPK-QPSALNNI  112 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHHH
Confidence            345677888889999999999999999987543332  457788888999999999999999999886432 23344444


Q ss_pred             HHHHHhcCCCCCCchhhHHHHHHHHHHcCCC-------hhHHHHHHHhcccCChhhHHHHHHHHHhcCCC
Q 040338          217 IDMYLKCGCNGIESSIQIGKALVTMYAEGGS-------TQKADLAFELMSRRNMISWMVLISAFSQAGVL  279 (385)
Q Consensus       217 i~~~~~~g~~~~~~~~~~~~~li~~~~~~g~-------~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~  279 (385)
                      ...|...|+..               ...|+       +++|.++++.....+...|..++..+...|+.
T Consensus       113 g~~~~~~g~~~---------------~a~~~~~~A~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~  167 (172)
T PRK02603        113 AVIYHKRGEKA---------------EEAGDQDEAEALFDKAAEYWKQAIRLAPNNYIEAQNWLKTTGRS  167 (172)
T ss_pred             HHHHHHcCChH---------------hHhhCHHHHHHHHHHHHHHHHHHHhhCchhHHHHHHHHHhcCcc
Confidence            44444433211               11122       46677777776666666677777777666653

>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=97.17  E-value=0.0009  Score=43.73  Aligned_cols=59  Identities=12%  Similarity=0.130  Sum_probs=42.4

Q ss_pred             ccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGAL  355 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~l  355 (385)
                      ..|++++|.++|+.+....+  ......+..+|.+.|++++|.++++.+... |+...|..+
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l   64 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQL   64 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            46778888888888777776  666667888888888888888888887764 664444443

...

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.14  E-value=0.0035  Score=53.20  Aligned_cols=97  Identities=9%  Similarity=-0.082  Sum_probs=76.8

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC----cchHHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT----CVIWGALL  356 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~----~~~~~~li  356 (385)
                      .|...+....+.|++++|...|+.+.+..+     +..+.-+...|...|++++|...|+.+... |+    ...+-.+.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg  224 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG  224 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence            344444444566889999999999998877     457777899999999999999999999764 43    33445566


Q ss_pred             HHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          357 GACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ..+...|+.++|...++++++..|...
T Consensus       225 ~~~~~~g~~~~A~~~~~~vi~~yP~s~  251 (263)
T PRK10803        225 VIMQDKGDTAKAKAVYQQVIKKYPGTD  251 (263)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCcCCH
Confidence            778899999999999999998887653

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.08  E-value=0.051  Score=45.75  Aligned_cols=185  Identities=10%  Similarity=-0.063  Sum_probs=106.0

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHh--hHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHh
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSM--LYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLK  222 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  222 (385)
                      .....+.+.|++++|.+.|+++...-..+...  ..-.+..++.+.+++++|...+++.++..+.....-|.-.+.+.+.
T Consensus        37 ~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~  116 (243)
T PRK10866         37 ATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTN  116 (243)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhh
Confidence            34455677899999999999998853222111  1235667889999999999999999998765544454444444332


Q ss_pred             --cCCCCCCchhhHHHHHHHHHHc----CCC---hhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHHHHH
Q 040338          223 --CGCNGIESSIQIGKALVTMYAE----GGS---TQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFFVSL  291 (385)
Q Consensus       223 --~g~~~~~~~~~~~~~li~~~~~----~g~---~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l  291 (385)
                        .+.           ..+..+..    ..|   ..+|+..|+.+.+  |+.. |.....-....-+-.-|.   .--.+
T Consensus       117 ~~~~~-----------~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~-ya~~A~~rl~~l~~~la~---~e~~i  181 (243)
T PRK10866        117 MALDD-----------SALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQ-YTTDATKRLVFLKDRLAK---YELSV  181 (243)
T ss_pred             hhcch-----------hhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCCh-hHHHHHHHHHHHHHHHHH---HHHHH
Confidence              110           00001100    011   2234445555444  3221 100000000000000000   11134


Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      ..-|.+.|.+..|..-++.+.+..+     ......++.+|...|..++|.++.....
T Consensus       182 a~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        182 AEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            4556777888888888888887777     6666778899999999999988776543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.08  E-value=0.02  Score=45.21  Aligned_cols=124  Identities=9%  Similarity=-0.071  Sum_probs=81.5

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC--CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGL--SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      ...|..+...+...|++++|+..|++.......|  ...++..+...+...|++++|+..++....... .....+..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~-~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNP-FLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CcHHHHHHHH
Confidence            4567778888889999999999999998753333  235788888899999999999999999987632 2233343443


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHH-------HHHHHhcccCChhhHHHHHHHHHhcCCC
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKA-------DLAFELMSRRNMISWMVLISAFSQAGVL  279 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A-------~~~~~~m~~~~~~~~~~li~~~~~~g~~  279 (385)
                      ..+.               .+.+.+...|+++.|       ..+|+.....+...+......+...|++
T Consensus       114 ~i~~---------------~~~~~~~~~g~~~~A~~~~~~a~~~~~~a~~~~p~~~~~~~~~~~~~~~~  167 (168)
T CHL00033        114 VICH---------------YRGEQAIEQGDSEIAEAWFDQAAEYWKQAIALAPGNYIEAQNWLKITGRF  167 (168)
T ss_pred             HHHH---------------HhhHHHHHcccHHHHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHhcCC
Confidence            3333               223344577777744       4445455445555555555545544443

>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=97.07  E-value=0.0058  Score=47.00  Aligned_cols=109  Identities=14%  Similarity=0.118  Sum_probs=50.1

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHh--cc-CCCc------------------hHHHhHHHHHHhcCChhHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKF--YF-VSDE------------------SIAKSSIDMHVKCGAVDYAES  108 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~--g~-~~~~------------------~~~~~li~~~~~~g~~~~a~~  108 (385)
                      ..|..++.........++.+.+...+.++...  |. -|+.                  .+...++..+...|++++|.+
T Consensus         4 ~~F~~~~~~a~~~~~~~~~~~~~~~~~~al~ly~G~~l~~~~~~~W~~~~r~~l~~~~~~~~~~l~~~~~~~~~~~~a~~   83 (146)
T PF03704_consen    4 DRFEALVREARAAARAGDPEEAIELLEEALALYRGDFLPDLDDEEWVEPERERLRELYLDALERLAEALLEAGDYEEALR   83 (146)
T ss_dssp             HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHH
Confidence            34444544333233356777777777777653  21 1111                  112233334444555555555


Q ss_pred             HHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH-----CCCCCCHhh
Q 040338          109 AFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN-----HGFGLSSML  177 (385)
Q Consensus       109 ~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~g~~p~~~t  177 (385)
                      +++++...+                   +.|...|-.+|.+|...|+..+|.++|+++.+     .|+.|+..|
T Consensus        84 ~~~~~l~~d-------------------P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   84 LLQRALALD-------------------PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHS-------------------TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHhcC-------------------CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            555554444                   24555555666666666666666655555432     355555443

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.02  E-value=0.0059  Score=48.50  Aligned_cols=96  Identities=8%  Similarity=0.005  Sum_probs=68.7

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGAC  359 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~  359 (385)
                      .+..+...+...|++++|...|++..+...     ...+..+...+.+.|++++|.+.+++.... | +...+..+...|
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~  116 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAVIY  116 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            455555666667777777788877765433     356777888889999999999998887763 4 445566677777


Q ss_pred             HhcCC--------------hHHHHHHHHHHHhccccC
Q 040338          360 CSHYN--------------TKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       360 ~~~g~--------------~~~a~~~~~~~~~~~~~~  382 (385)
                      ...|+              +++|.+.+++....+|.+
T Consensus       117 ~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~~p~~  153 (172)
T PRK02603        117 HKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRLAPNN  153 (172)
T ss_pred             HHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhhCchh
Confidence            77766              567778888777776653

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.02  E-value=0.22  Score=44.23  Aligned_cols=211  Identities=12%  Similarity=-0.027  Sum_probs=120.4

Q ss_pred             HHHHHHHHHHHHhccCCC---chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHH
Q 040338           69 KMALHLHGLVKKFYFVSD---ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNT  145 (385)
Q Consensus        69 ~~a~~~~~~m~~~g~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  145 (385)
                      ++..+.+..|.++=-.|+   ..+.-.++-.|....+++...++++.+......             + . .....+--.
T Consensus       120 ~~l~~~L~~i~~rLd~~~~ls~div~~lllSyRdiqdydamI~Lve~l~~~p~~-------------~-~-~~~~~i~~~  184 (374)
T PF13281_consen  120 KELAKELRRIRQRLDDPELLSPDIVINLLLSYRDIQDYDAMIKLVETLEALPTC-------------D-V-ANQHNIKFQ  184 (374)
T ss_pred             HHHHHHHHHHHHhhCCHhhcChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCcc-------------c-h-hcchHHHHH
Confidence            444455555555421222   333345555788889999999999998764210             0 0 112222223


Q ss_pred             HHHHHHh---CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHh
Q 040338          146 MISILTR---HGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLK  222 (385)
Q Consensus       146 li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  222 (385)
                      ...++.+   .|+.++|++++..+....-.++..||..+.+.|-+.             -..+...+......-+.+|.+
T Consensus       185 yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GRIyKD~-------------~~~s~~~d~~~ldkAi~~Y~k  251 (374)
T PF13281_consen  185 YAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGRIYKDL-------------FLESNFTDRESLDKAIEWYRK  251 (374)
T ss_pred             HHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHH-------------HHHcCccchHHHHHHHHHHHH
Confidence            4456667   899999999999977666778888988887665321             111111222233344444443


Q ss_pred             cCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChh
Q 040338          223 CGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVT  302 (385)
Q Consensus       223 ~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~  302 (385)
                      .=..+  |+...--++...+.-.|.-.+...-..++.       ..+-....+.|..+.....|-+.++++++.-.|+.+
T Consensus       252 gFe~~--~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~-------~~l~~llg~kg~~~~~~dYWd~ATl~Ea~vL~~d~~  322 (374)
T PF13281_consen  252 GFEIE--PDYYSGINAATLLMLAGHDFETSEELRKIG-------VKLSSLLGRKGSLEKMQDYWDVATLLEASVLAGDYE  322 (374)
T ss_pred             HHcCC--ccccchHHHHHHHHHcCCcccchHHHHHHH-------HHHHHHHHhhccccccccHHHHHHHHHHHHHcCCHH
Confidence            32222  222222222222333333222111111111       223334567788888888899999999999999999


Q ss_pred             hHHHHHHHHHhccc
Q 040338          303 KGKHYFTAMAKFTY  316 (385)
Q Consensus       303 ~a~~~~~~~~~~~~  316 (385)
                      +|.+..+.|.+..+
T Consensus       323 ka~~a~e~~~~l~~  336 (374)
T PF13281_consen  323 KAIQAAEKAFKLKP  336 (374)
T ss_pred             HHHHHHHHHhhcCC
Confidence            99999999988765

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.01  E-value=0.0024  Score=53.57  Aligned_cols=88  Identities=16%  Similarity=0.073  Sum_probs=56.7

Q ss_pred             cccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELV  371 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~  371 (385)
                      .+.+++.+|...|.+.++..+  ...|.--..+|++.|.++.|++-.+....- | -..+|.+|..+|...|++.+|.+.
T Consensus        92 m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~a  171 (304)
T KOG0553|consen   92 MKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIEA  171 (304)
T ss_pred             HHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHHH
Confidence            345666666666777666666  555666666677777777776666665542 3 244677777777777777777777


Q ss_pred             HHHHHhccccCC
Q 040338          372 MRNLLQLDVKVF  383 (385)
Q Consensus       372 ~~~~~~~~~~~~  383 (385)
                      |++.++.+|.+.
T Consensus       172 ykKaLeldP~Ne  183 (304)
T KOG0553|consen  172 YKKALELDPDNE  183 (304)
T ss_pred             HHhhhccCCCcH
Confidence            777766666543

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.99  E-value=0.15  Score=45.19  Aligned_cols=187  Identities=11%  Similarity=-0.071  Sum_probs=113.3

Q ss_pred             CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhc---cCCCchHHHhHHHHHHh---cCChhHHHHHHHhccCCCcc
Q 040338           46 PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFY---FVSDESIAKSSIDMHVK---CGAVDYAESAFLRMLNPSLF  119 (385)
Q Consensus        46 ~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g---~~~~~~~~~~li~~~~~---~g~~~~a~~~~~~m~~~~~~  119 (385)
                      .|+..+-..++.-+..+....+++...++.+.+....   +.-...+-....-++.+   .|+-++|++++..+..+.. 
T Consensus       135 ~~~~ls~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~-  213 (374)
T PF13281_consen  135 DPELLSPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDE-  213 (374)
T ss_pred             CHhhcChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccC-
Confidence            3444444445554444555899999999999998741   11123333345567777   8999999999988543333 


Q ss_pred             ccccchHHHHHHhcCCCCCCcchHHHHHHHHHh---------CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccC
Q 040338          120 CWKFGIIRLLIMFQKMPERDLVSWNTMISILTR---------HGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYD  190 (385)
Q Consensus       120 ~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~---------~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~  190 (385)
                                       .++..+|..+...|-.         ....++|++.|.+--+.  .||..+=-.+...+.-.|.
T Consensus       214 -----------------~~~~d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~  274 (374)
T PF13281_consen  214 -----------------NPDPDTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGH  274 (374)
T ss_pred             -----------------CCChHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCC
Confidence                             5777788777765432         22467788888876553  4655443333333333333


Q ss_pred             ccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCCh
Q 040338          191 LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNM  263 (385)
Q Consensus       191 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~  263 (385)
                      ..+...-.+++.           ..+-..+.+.|..+...+--.+.+++.+..-.|+.++|.+..+.|.+.+.
T Consensus       275 ~~~~~~el~~i~-----------~~l~~llg~kg~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~  336 (374)
T PF13281_consen  275 DFETSEELRKIG-----------VKLSSLLGRKGSLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKP  336 (374)
T ss_pred             cccchHHHHHHH-----------HHHHHHHHhhccccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCC
Confidence            222221111111           12223344555555555666677888899999999999999999986433

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.96  E-value=0.016  Score=45.76  Aligned_cols=95  Identities=17%  Similarity=0.021  Sum_probs=67.0

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCC--CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVS--DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      ..|..+...+..   .|++++|...++........+  ...++..+..+|...|+.++|+..+++..+..          
T Consensus        36 ~~~~~~g~~~~~---~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~----------  102 (168)
T CHL00033         36 FTYYRDGMSAQS---EGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN----------  102 (168)
T ss_pred             HHHHHHHHHHHH---cCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----------
Confidence            344555555444   899999999999998764332  23578889999999999999999998876543          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHH-------hCCCchHHHHHHHHH
Q 040338          128 LLIMFQKMPERDLVSWNTMISILT-------RHGFGFETLCTFIEL  166 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~-------~~~~~~~a~~~~~~m  166 (385)
                               +....+++.+...+.       ..|+++.|+..+++.
T Consensus       103 ---------~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        103 ---------PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             ---------cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence                     234455666666666       677777665555543

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.95  E-value=0.17  Score=42.60  Aligned_cols=176  Identities=12%  Similarity=0.079  Sum_probs=118.1

Q ss_pred             HHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcc
Q 040338          180 TAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMS  259 (385)
Q Consensus       180 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  259 (385)
                      .....+...|++++|.+.|+.+....+.+.....                    ..-.+..++.+.+++++|...+++..
T Consensus        37 ~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~--------------------a~l~la~ayy~~~~y~~A~~~~e~fi   96 (243)
T PRK10866         37 ATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQ--------------------VQLDLIYAYYKNADLPLAQAAIDRFI   96 (243)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHH--------------------HHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            3444556789999999999999987553322111                    12345677888999999999999987


Q ss_pred             c--CC--hhhHHHHHHHHHh--cC---------------CCCchHHHH-HHHHHHHHhcccCChhhHHHHHHHHHhccch
Q 040338          260 R--RN--MISWMVLISAFSQ--AG---------------VLEKPRFFF-FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYT  317 (385)
Q Consensus       260 ~--~~--~~~~~~li~~~~~--~g---------------~~~~a~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  317 (385)
                      +  |+  -..|...+.+.+.  .+               +...+.+-+ .+..++.-|-.+.-..+|...+..+...-- 
T Consensus        97 ~~~P~~~~~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la-  175 (243)
T PRK10866         97 RLNPTHPNIDYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLA-  175 (243)
T ss_pred             HhCcCCCchHHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHH-
Confidence            6  32  2334444444331  11               111233333 677888888877777777766665543322 


Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcc----hHHHHHHHHHhcCChHHHHHHHHHHH
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCV----IWGALLGACCSHYNTKLAELVMRNLL  376 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~----~~~~li~~~~~~g~~~~a~~~~~~~~  376 (385)
                      ..--...+.|.+.|++..|..-++.+.++ |+..    ..-.++.+|...|..++|....+-+.
T Consensus       176 ~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        176 KYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            22224667789999999999999998876 5443    45578899999999999998876654

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.92  E-value=0.0067  Score=46.31  Aligned_cols=82  Identities=7%  Similarity=0.007  Sum_probs=45.9

Q ss_pred             ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHH
Q 040338          262 NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLL  327 (385)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~  327 (385)
                      +......+..-+...|++++|..+|            -|-.|..+|...|++++|+..|.......+  +..+-.+..++
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~  113 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            3334444444445555555555554            344455555555666666666666655555  55555566666


Q ss_pred             HccCCHHHHHHHHHhC
Q 040338          328 GLSGLLGEAKKLIDEM  343 (385)
Q Consensus       328 ~~~g~~~~A~~~~~~m  343 (385)
                      ...|+.+.|.+-|+..
T Consensus       114 L~lG~~~~A~~aF~~A  129 (157)
T PRK15363        114 LACDNVCYAIKALKAV  129 (157)
T ss_pred             HHcCCHHHHHHHHHHH
Confidence            6666666666666543

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.91  E-value=0.023  Score=52.72  Aligned_cols=211  Identities=14%  Similarity=0.056  Sum_probs=115.0

Q ss_pred             HHHHHHHHHhCCC--chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          143 WNTMISILTRHGF--GFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       143 ~~~li~~~~~~~~--~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      ++..=.+|.+..+  +-+.+.-+++|++.|-.|+....   ...|+-.|.+.+|-++|.+   .|.+..      .+.+|
T Consensus       601 f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iLl---A~~~Ay~gKF~EAAklFk~---~G~enR------AlEmy  668 (1081)
T KOG1538|consen  601 FETARKAYIRVRDLRYLELISELEERKKRGETPNDLLL---ADVFAYQGKFHEAAKLFKR---SGHENR------ALEMY  668 (1081)
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHHH---HHHHHhhhhHHHHHHHHHH---cCchhh------HHHHH
Confidence            4555566665544  44556667778888888887653   3345556778777777654   343211      11111


Q ss_pred             HhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHH------------
Q 040338          221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFF------------  286 (385)
Q Consensus       221 ~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~------------  286 (385)
                      ....         +| -...-+...|..++-..+.++=.+  .|+.--.+-.+.+...|+.++|..+.            
T Consensus       669 TDlR---------MF-D~aQE~~~~g~~~eKKmL~RKRA~WAr~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI  738 (1081)
T KOG1538|consen  669 TDLR---------MF-DYAQEFLGSGDPKEKKMLIRKRADWARNIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDI  738 (1081)
T ss_pred             HHHH---------HH-HHHHHHhhcCChHHHHHHHHHHHHHhhhcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHH
Confidence            1100         00 011112222222222222211110  11111123345566777777777766            


Q ss_pred             ----------HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcc-----
Q 040338          287 ----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCV-----  350 (385)
Q Consensus       287 ----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~-----  350 (385)
                                +...+..-+.+...+..|.++|.+|..      ..++++.....++|++|..+-+..++- ||+.     
T Consensus       739 ~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD------~ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaq  812 (1081)
T KOG1538|consen  739 ARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGD------LKSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQ  812 (1081)
T ss_pred             HhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhcc------HHHHhhheeecccchHhHhhhhhCccccccccchHHH
Confidence                      222333333334444555555555432      345777888899999999999888773 4432     


Q ss_pred             ------hHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          351 ------IWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       351 ------~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                            -|...-.+|.+.|+..+|.++++++....+.
T Consensus       813 wLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLtnnav~  849 (1081)
T KOG1538|consen  813 WLAENDRFEEAQKAFHKAGRQREAVQVLEQLTNNAVA  849 (1081)
T ss_pred             HhhhhhhHHHHHHHHHHhcchHHHHHHHHHhhhhhhh
Confidence                  3445667899999999999999998765443

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.89  E-value=0.058  Score=41.30  Aligned_cols=85  Identities=8%  Similarity=-0.197  Sum_probs=68.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|..+|+.+....+. +..-|-.|.-++-..|++++|+..|......+                   +.|..++-
T Consensus        48 ~G~l~~A~~~f~~L~~~Dp~-~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-------------------~ddp~~~~  107 (157)
T PRK15363         48 VKEFAGAARLFQLLTIYDAW-SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-------------------IDAPQAPW  107 (157)
T ss_pred             CCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-------------------CCCchHHH
Confidence            79999999999998886432 55666777777778899999999998876655                   46777888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      .+-.++...|+.+.|.+.|+.....
T Consensus       108 ~ag~c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        108 AAAECYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            8888899999999999998877654

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.87  E-value=0.033  Score=40.88  Aligned_cols=110  Identities=9%  Similarity=-0.020  Sum_probs=76.8

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHCCCCCC--HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          146 MISILTRHGFGFETLCTFIELWNHGFGLS--SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       146 li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      +-.++-..|+.++|+.+|++....|+...  ...+-.+.+.+...|++++|..+++......+.++.             
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~-------------   73 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDEL-------------   73 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccc-------------
Confidence            34566778999999999999999887765  345566777888999999999999988876432111             


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHh
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQ  275 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~  275 (385)
                             +......+..++...|+.++|+..+-...-++...|..-|..|..
T Consensus        74 -------~~~l~~f~Al~L~~~gr~~eAl~~~l~~la~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   74 -------NAALRVFLALALYNLGRPKEALEWLLEALAETLPRYRRAIRFYAD  118 (120)
T ss_pred             -------cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence                   111112233466677888888888876665666677666666653

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.85  E-value=0.023  Score=53.30  Aligned_cols=142  Identities=9%  Similarity=-0.077  Sum_probs=97.2

Q ss_pred             CCchhhHHHHHHHHHHcCC-----ChhHHHHHHHhccc--CC-hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccC
Q 040338          228 IESSIQIGKALVTMYAEGG-----STQKADLAFELMSR--RN-MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSG  299 (385)
Q Consensus       228 ~~~~~~~~~~li~~~~~~g-----~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~  299 (385)
                      .+.+...|...+++.....     +.+.|..+|++..+  |+ ...|..+..++.....+...              ...
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~--------------~~~  398 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPL--------------DEK  398 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCc--------------cHH
Confidence            4566677888877765432     36789999988876  43 34555554444332222110              011


Q ss_pred             ChhhHHHHHHHHHhc--cc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          300 PVTKGKHYFTAMAKF--TY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPTCVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~--~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      ++..+.+........  ..  +..+.++.-.....|++++|...+++... +|+...|..+...|...|+.++|.+.+++
T Consensus       399 ~l~~a~~~~~~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~  478 (517)
T PRK10153        399 QLAALSTELDNIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYST  478 (517)
T ss_pred             HHHHHHHHHHHhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            234444444443332  11  56677776667778999999999999887 48888999999999999999999999999


Q ss_pred             HHhccccCC
Q 040338          375 LLQLDVKVF  383 (385)
Q Consensus       375 ~~~~~~~~~  383 (385)
                      ...++|.++
T Consensus       479 A~~L~P~~p  487 (517)
T PRK10153        479 AFNLRPGEN  487 (517)
T ss_pred             HHhcCCCCc
Confidence            999998865

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=96.84  E-value=0.0041  Score=40.15  Aligned_cols=56  Identities=21%  Similarity=0.210  Sum_probs=37.0

Q ss_pred             HHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338           94 IDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus        94 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      ...+.+.|++++|.+.|++..+.+                   +.+...+..+..++...|++++|...|++..+
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~-------------------P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD-------------------PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS-------------------TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445666777777777777766655                   24566666677777777777777777777655

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

Probab=96.80  E-value=0.0099  Score=51.27  Aligned_cols=131  Identities=16%  Similarity=0.080  Sum_probs=72.0

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHh-hhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHH
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVR-CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFL  111 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~-~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~  111 (385)
                      .++.|+.+|.+.......+|...+....- ....++.+.|.++|+...+. ++.+...|...++.+.+.++.+.|..+|+
T Consensus        16 g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l~~~~d~~~aR~lfe   94 (280)
T PF05843_consen   16 GIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFLIKLNDINNARALFE   94 (280)
T ss_dssp             HHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             ChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHhCcHHHHHHHHH
Confidence            66777777776654333333333321111 11146666677777777665 45566667777777777777777777777


Q ss_pred             hccCCCccccccchHHHHHHhcCCCCC-CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040338          112 RMLNPSLFCWKFGIIRLLIMFQKMPER-DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS  183 (385)
Q Consensus       112 ~m~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  183 (385)
                      +....-.                 ... ....|...+..=.+.|+.+.+.++.+++.+.  -|+......+++
T Consensus        95 r~i~~l~-----------------~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~  148 (280)
T PF05843_consen   95 RAISSLP-----------------KEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSD  148 (280)
T ss_dssp             HHCCTSS-----------------CHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHC
T ss_pred             HHHHhcC-----------------chhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHH
Confidence            6654311                 011 2346777777777777777777777777663  444444444443

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.

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=96.76  E-value=0.0028  Score=55.36  Aligned_cols=236  Identities=11%  Similarity=-0.027  Sum_probs=137.3

Q ss_pred             hHHHHH--HHHHhCCCchHHHHHHHHHHHCCCC---CCHhhHHHHHHHhcCccCccchhhHHHHHHH----hCCCCc-h-
Q 040338          142 SWNTMI--SILTRHGFGFETLCTFIELWNHGFG---LSSMLYATAFSARASVYDLEWGPHLHSRVVH----MEPSLD-V-  210 (385)
Q Consensus       142 ~~~~li--~~~~~~~~~~~a~~~~~~m~~~g~~---p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~----~~~~~~-~-  210 (385)
                      ++...+  .-+|+.|+....+.+|+...+.|..   .=...|..|-++|.-.+++++|.+++..=+-    .|-+.. . 
T Consensus        17 CleLalEGERLck~gdcraGv~ff~aA~qvGTeDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAK   96 (639)
T KOG1130|consen   17 CLELALEGERLCKMGDCRAGVDFFKAALQVGTEDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAK   96 (639)
T ss_pred             HHHHHHHHHHHHhccchhhhHHHHHHHHHhcchHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhcccc
Confidence            444444  3468888888888888888877633   2234566667777777788888776543210    010000 0 


Q ss_pred             ------------HHHHHHHHHHHhcCCCC-----CCchhhHHHHHHHHHHcCCC--------------------hhHHHH
Q 040338          211 ------------FVGSGLIDMYLKCGCNG-----IESSIQIGKALVTMYAEGGS--------------------TQKADL  253 (385)
Q Consensus       211 ------------~~~~~li~~~~~~g~~~-----~~~~~~~~~~li~~~~~~g~--------------------~~~A~~  253 (385)
                                  -.|+..+.++.+.=++.     .......+-.+...|...|+                    ++.|.+
T Consensus        97 ssgNLGNtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~  176 (639)
T KOG1130|consen   97 SSGNLGNTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVK  176 (639)
T ss_pred             ccccccchhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHH
Confidence                        01111111111110000     12223344455555554432                    223444


Q ss_pred             HHHhccc---------CChhhHHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCChhhHHH
Q 040338          254 AFELMSR---------RNMISWMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKH  306 (385)
Q Consensus       254 ~~~~m~~---------~~~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~  306 (385)
                      +|.+=.+         .-...|..|...|.-.|+++.|+..-                  ++..+..++.-.|+++.|.+
T Consensus       177 fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~e  256 (639)
T KOG1130|consen  177 FYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIE  256 (639)
T ss_pred             HHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHH
Confidence            4432211         01235555556666667777776554                  78888888888999999988


Q ss_pred             HHHHHHhcc----c----hhhHHHHHHHHHccCCHHHHHHHHHhCCC-------C-CCcchHHHHHHHHHhcCChHHHHH
Q 040338          307 YFTAMAKFT----Y----TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-------K-PTCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       307 ~~~~~~~~~----~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~-p~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      .|+.....-    .    ....-+|...|.-...++.|+..+.+-..       . -....|-+|.++|...|..++|+.
T Consensus       257 hYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~  336 (639)
T KOG1130|consen  257 HYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALY  336 (639)
T ss_pred             HHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHH
Confidence            887654322    2    44555677777777788888887754432       1 455678889999999999999988


Q ss_pred             HHHHHHh
Q 040338          371 VMRNLLQ  377 (385)
Q Consensus       371 ~~~~~~~  377 (385)
                      +.+.-++
T Consensus       337 fae~hl~  343 (639)
T KOG1130|consen  337 FAELHLR  343 (639)
T ss_pred             HHHHHHH
Confidence            8776554

>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=96.76  E-value=0.0022  Score=42.02  Aligned_cols=63  Identities=16%  Similarity=0.010  Sum_probs=50.3

Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC-ChHHHHHHHHHHHhccc
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY-NTKLAELVMRNLLQLDV  380 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~  380 (385)
                      ..+..+...+...|++++|+..|++..+. | +...|..+..+|...| ++++|++.+++.++.+|
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            45667778888888899998888887763 4 5567888888888888 68999999988887765

...

>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=96.72  E-value=0.0062  Score=39.68  Aligned_cols=52  Identities=19%  Similarity=0.139  Sum_probs=44.9

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCC
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPS  117 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  117 (385)
                      .|++++|.++|+.+.+.. +-+...+..+..+|.+.|++++|.++++++...+
T Consensus         4 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~   55 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQD   55 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG
T ss_pred             ccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            799999999999999875 3377888889999999999999999999887655

...

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.69  E-value=0.012  Score=49.03  Aligned_cols=117  Identities=9%  Similarity=-0.014  Sum_probs=90.4

Q ss_pred             hhhhHHHHHhhhC--CCChhhHHHHHHHHHhh--hccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcC-------
Q 040338           33 LIDDDYRVFCDIG--PRYLFTYNTMINGGVRC--LCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCG-------  101 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~--~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g-------  101 (385)
                      ++-...+.|...+  ++|-.+|-+++..|..-  .++++++-....+..|.+.|+.-|..+|+.||+.+-+..       
T Consensus        49 ~Lv~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvf  128 (406)
T KOG3941|consen   49 SLVHVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVF  128 (406)
T ss_pred             cccchhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHH
Confidence            4444556677666  67888899999888753  446888888999999999999999999999999886643       


Q ss_pred             ---------ChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCch-HHHHHHHHHH
Q 040338          102 ---------AVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGF-ETLCTFIELW  167 (385)
Q Consensus       102 ---------~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~-~a~~~~~~m~  167 (385)
                               +-+-+++++++|...|+                  -||-.+-..|++++.+.+.+- +..+++-.|-
T Consensus       129 Q~~F~HYP~QQ~C~I~vLeqME~hGV------------------mPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  129 QKVFLHYPQQQNCAIKVLEQMEWHGV------------------MPDKEIEDILVNAFGRWNFPTKKVKRMLYWMP  186 (406)
T ss_pred             HHHHhhCchhhhHHHHHHHHHHHcCC------------------CCchHHHHHHHHHhccccccHHHHHHHHHhhh
Confidence                     23446778888888887                  799999999999999888654 3444444443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.63  E-value=0.091  Score=49.44  Aligned_cols=141  Identities=9%  Similarity=-0.064  Sum_probs=98.2

Q ss_pred             CCChhhHHHHHHHHHhhh--ccCChHHHHHHHHHHHHhccCCC-chHHHhHHHHHHhcCC--------hhHHHHHHHhcc
Q 040338           46 PRYLFTYNTMINGGVRCL--CVGNIKMALHLHGLVKKFYFVSD-ESIAKSSIDMHVKCGA--------VDYAESAFLRML  114 (385)
Q Consensus        46 ~~~~~~~~~li~~~~~~~--~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~--------~~~a~~~~~~m~  114 (385)
                      ..|...|...+++.....  ..+....|..+|++..+.  .|+ ...|..+..++.....        +..+.+...+..
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            567889999999966421  234588999999999986  444 4555555444433211        122222222211


Q ss_pred             CCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccch
Q 040338          115 NPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWG  194 (385)
Q Consensus       115 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a  194 (385)
                      ...                 ..+.+...|.++.-.....|++++|...+++....  .|+...|..+...+...|+.++|
T Consensus       412 al~-----------------~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L--~ps~~a~~~lG~~~~~~G~~~eA  472 (517)
T PRK10153        412 ALP-----------------ELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL--EMSWLNYVLLGKVYELKGDNRLA  472 (517)
T ss_pred             hcc-----------------cCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCHHHH
Confidence            110                 11345567887766667789999999999999985  57888999999999999999999


Q ss_pred             hhHHHHHHHhCCC
Q 040338          195 PHLHSRVVHMEPS  207 (385)
Q Consensus       195 ~~~~~~~~~~~~~  207 (385)
                      .+.+++..+..+.
T Consensus       473 ~~~~~~A~~L~P~  485 (517)
T PRK10153        473 ADAYSTAFNLRPG  485 (517)
T ss_pred             HHHHHHHHhcCCC
Confidence            9999999887654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.62  E-value=0.0047  Score=40.95  Aligned_cols=59  Identities=12%  Similarity=-0.006  Sum_probs=40.6

Q ss_pred             HHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          325 DLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       325 ~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ..|.+.+++++|.++++.+... | +...|......+...|++++|.+.+++..+.+|.++
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~   63 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSPDDP   63 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcH
Confidence            4566777777777777777663 3 445566677777777777777777777777766543

>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=96.53  E-value=0.04  Score=40.90  Aligned_cols=94  Identities=11%  Similarity=-0.047  Sum_probs=56.5

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCC--CCCCcchHHHHHHHHHhCCCchHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKM--PERDLVSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~--~~~~~~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                      |..++.++|.++++.|+++....+++..=..++......-.     +..-  ..|+..+..+++.+|+.+|++..|++++
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~-----~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~v   75 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGD-----YPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLV   75 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCc-----cCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHH
Confidence            45778889999999999998888887663222100000000     0000  1366666777777777777777777777


Q ss_pred             HHHHH-CCCCCCHhhHHHHHHH
Q 040338          164 IELWN-HGFGLSSMLYATAFSA  184 (385)
Q Consensus       164 ~~m~~-~g~~p~~~t~~~ll~~  184 (385)
                      +...+ .+++.+..++..|+.=
T Consensus        76 d~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   76 DFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHH
Confidence            66644 3555566666666553

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

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.53  E-value=0.45  Score=44.68  Aligned_cols=95  Identities=8%  Similarity=-0.004  Sum_probs=54.5

Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHHhccc----------
Q 040338          251 ADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----------  316 (385)
Q Consensus       251 A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----------  316 (385)
                      +.++-.++...+..+...+..-+.+...+.-|-++|    -...++......++|++|..+-+...+.-.          
T Consensus       735 lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwL  814 (1081)
T KOG1538|consen  735 LIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGDLKSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWL  814 (1081)
T ss_pred             HHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhccHHHHhhheeecccchHhHhhhhhCccccccccchHHHHh
Confidence            333333333333444444444444455555555555    344556666677777777776666554332          


Q ss_pred             --hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          317 --TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       317 --~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                        ..-|.---++|.++|+-.||.++++++..
T Consensus       815 AE~DrFeEAqkAfhkAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  815 AENDRFEEAQKAFHKAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             hhhhhHHHHHHHHHHhcchHHHHHHHHHhhh
Confidence              22333445677888888888888888765

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.52  E-value=0.58  Score=42.09  Aligned_cols=86  Identities=12%  Similarity=0.143  Sum_probs=60.9

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHH-HHHHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWG-ALLGACC  360 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~-~li~~~~  360 (385)
                      +|...+.+-.+..-++.|+.+|.+..+.+.    ..++++++.-++ .|+...|.++|+-=... ||...|. -.+..+.
T Consensus       399 v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~fLi  477 (660)
T COG5107         399 VFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPDSTLYKEKYLLFLI  477 (660)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCCchHHHHHHHHHHH
Confidence            778888888888889999999999999885    667788887766 56677777877644433 5555443 2444455


Q ss_pred             hcCChHHHHHHHH
Q 040338          361 SHYNTKLAELVMR  373 (385)
Q Consensus       361 ~~g~~~~a~~~~~  373 (385)
                      ..++-..|..+|+
T Consensus       478 ~inde~naraLFe  490 (660)
T COG5107         478 RINDEENARALFE  490 (660)
T ss_pred             HhCcHHHHHHHHH
Confidence            5666666666666

>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=96.46  E-value=0.055  Score=40.17  Aligned_cols=86  Identities=13%  Similarity=-0.031  Sum_probs=71.4

Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHH---------------CCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHH
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWN---------------HGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVH  203 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---------------~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~  203 (385)
                      |..++.++|.++++.|+.+....+++..-.               ..+.|+..+..+++.+|+..+++..|.++.+...+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            456788999999999999999999877521               12568899999999999999999999999999988


Q ss_pred             h-CCCCchHHHHHHHHHHHhcC
Q 040338          204 M-EPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       204 ~-~~~~~~~~~~~li~~~~~~g  224 (385)
                      . +++.+..+|..|++......
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v~s  102 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYVLS  102 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHHhc
Confidence            6 67777888888888765544

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

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.35  E-value=0.032  Score=46.98  Aligned_cols=96  Identities=8%  Similarity=-0.030  Sum_probs=60.7

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .+++++|+..|.+.++.. +-|.+-|..-..+|++.|..+.|++=.+.....+                   +.-..+|.
T Consensus        94 ~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-------------------p~yskay~  153 (304)
T KOG0553|consen   94 NKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID-------------------PHYSKAYG  153 (304)
T ss_pred             hhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-------------------hHHHHHHH
Confidence            566777777777776653 2355566666677777777777766665555444                   23345677


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAF  182 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll  182 (385)
                      .|-.+|...|++++|++.|.+..+  +.|+-.+|-.=+
T Consensus       154 RLG~A~~~~gk~~~A~~aykKaLe--ldP~Ne~~K~nL  189 (304)
T KOG0553|consen  154 RLGLAYLALGKYEEAIEAYKKALE--LDPDNESYKSNL  189 (304)
T ss_pred             HHHHHHHccCcHHHHHHHHHhhhc--cCCCcHHHHHHH
Confidence            777777777777777777766655  566665554433

>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=96.33  E-value=0.0076  Score=39.40  Aligned_cols=64  Identities=9%  Similarity=0.018  Sum_probs=51.4

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCC-CchHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHG-FGFETLCTFI  164 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~  164 (385)
                      +..+|..+...+...|++++|+..|++..+.+                   +.+...|..+..++.+.| ++++|++.++
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            45678888888888999999999988876655                   356778888888888888 6889988888


Q ss_pred             HHHH
Q 040338          165 ELWN  168 (385)
Q Consensus       165 ~m~~  168 (385)
                      +..+
T Consensus        63 ~al~   66 (69)
T PF13414_consen   63 KALK   66 (69)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8765

...

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.32  E-value=0.043  Score=40.31  Aligned_cols=85  Identities=15%  Similarity=0.026  Sum_probs=63.8

Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC---cc-hHHHHHHHHHh
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT---CV-IWGALLGACCS  361 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~---~~-~~~~li~~~~~  361 (385)
                      ..++-..|+.++|+.+|++....|.     ...+-.+...|...|++++|..+|++.... |+   .. ....+.-++..
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~   87 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYN   87 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHH
Confidence            3455667899999999999988876     455666888889999999999999888765 55   22 22334456788


Q ss_pred             cCChHHHHHHHHHHH
Q 040338          362 HYNTKLAELVMRNLL  376 (385)
Q Consensus       362 ~g~~~~a~~~~~~~~  376 (385)
                      .|+.++|++.+-...
T Consensus        88 ~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   88 LGRPKEALEWLLEAL  102 (120)
T ss_pred             CCCHHHHHHHHHHHH
Confidence            899999998876543

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.30  E-value=0.17  Score=47.83  Aligned_cols=67  Identities=12%  Similarity=-0.025  Sum_probs=37.0

Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC-CCCCCH--------hhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNH-GFGLSS--------MLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~--------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      .|.+..|..|.....+.-.++-|...|-+.... |++.-.        ..-..=+.+|  -|.+++|++++-++-+..
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~feeaek~yld~drrD  764 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDADRRD  764 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccchhh
Confidence            466777887776666666666666666554332 222100        0111112222  367888888887776654

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.28  E-value=0.45  Score=38.88  Aligned_cols=82  Identities=12%  Similarity=0.022  Sum_probs=54.4

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcc----hHHHHHHHHHh
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCV----IWGALLGACCS  361 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~----~~~~li~~~~~  361 (385)
                      .+..++.-|-.+.-..+|...+..+...- ...--.+.+.|.+.|.+..|..-++.+.+. |+..    ..-.++.+|.+
T Consensus       112 ~~~~li~~yP~S~y~~~A~~~l~~l~~~l-a~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~  190 (203)
T PF13525_consen  112 EFEELIKRYPNSEYAEEAKKRLAELRNRL-AEHELYIARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYK  190 (203)
T ss_dssp             HHHHHHHH-TTSTTHHHHHHHHHHHHHHH-HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCchHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHH
Confidence            56677777777777777776666654332 222223677789999999999988888775 6554    44678888888


Q ss_pred             cCChHHHH
Q 040338          362 HYNTKLAE  369 (385)
Q Consensus       362 ~g~~~~a~  369 (385)
                      .|..+.+.
T Consensus       191 l~~~~~a~  198 (203)
T PF13525_consen  191 LGLKQAAD  198 (203)
T ss_dssp             TT-HHHHH
T ss_pred             hCChHHHH
Confidence            88877544

>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=96.23  E-value=0.0051  Score=41.42  Aligned_cols=60  Identities=12%  Similarity=0.018  Sum_probs=42.7

Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCC-------C-CC-cchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPS-------K-PT-CVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      .+++.+...|...|++++|+..|++..+       . |+ ..++..+...|...|++++|++.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4566677777777777777777766543       1 32 45677888888888888888888888765

...

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.21  E-value=0.78  Score=40.30  Aligned_cols=85  Identities=13%  Similarity=0.125  Sum_probs=69.3

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTK  366 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~  366 (385)
                      +.+..+.-|...|+...|.++-.+. +-+....|-.-+.+|+..++|++..++-..   +.++.-|..++.+|.+.|+..
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~F-kv~dkrfw~lki~aLa~~~~w~eL~~fa~s---kKsPIGyepFv~~~~~~~~~~  254 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEF-KVPDKRFWWLKIKALAENKDWDELEKFAKS---KKSPIGYEPFVEACLKYGNKK  254 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHHhcCCHHHHHHHHhC---CCCCCChHHHHHHHHHCCCHH
Confidence            6677778888889988888886665 223367788899999999999999987654   335689999999999999999


Q ss_pred             HHHHHHHHH
Q 040338          367 LAELVMRNL  375 (385)
Q Consensus       367 ~a~~~~~~~  375 (385)
                      +|..+..++
T Consensus       255 eA~~yI~k~  263 (319)
T PF04840_consen  255 EASKYIPKI  263 (319)
T ss_pred             HHHHHHHhC
Confidence            999988774

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

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.19  E-value=0.046  Score=45.66  Aligned_cols=88  Identities=8%  Similarity=-0.007  Sum_probs=72.0

Q ss_pred             CCCcchHHHHHHHHHhC-----CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc----------------Cccchh
Q 040338          137 ERDLVSWNTMISILTRH-----GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY----------------DLEWGP  195 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~----------------~~~~a~  195 (385)
                      +.|-.+|-..+..+...     +..+-....+..|.+.|+.-|..+|+.|++.+=+..                +-+-++
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I  143 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAI  143 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHH
Confidence            45667777777776543     556667778889999999999999999999876543                345678


Q ss_pred             hHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          196 HLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      +++++|...|+.||..+-..|++++++.+
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~FGr~~  172 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNAFGRWN  172 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHHhcccc
Confidence            99999999999999999999999998887

>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=96.13  E-value=0.019  Score=38.52  Aligned_cols=57  Identities=11%  Similarity=0.040  Sum_probs=39.2

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhc-------cc--hhhHHHHHHHHHccCCHHHHHHHHHhC
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKF-------TY--TCYFVCMVDLLGLSGLLGEAKKLIDEM  343 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~--~~~~~~li~~~~~~g~~~~A~~~~~~m  343 (385)
                      +|+.+...|...|++++|+..+++..+.       ..  ..++..+...+...|++++|++.+++.
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3455555555566666666666555533       11  677888999999999999999999864

...

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.07  E-value=0.4  Score=37.72  Aligned_cols=109  Identities=9%  Similarity=0.048  Sum_probs=66.8

Q ss_pred             ChhhHHHHHHHHHhcCCCCchHHHH-------------HHHHHHHHhcccCChhhHHHHHHHHHhccc----hhhHHHHH
Q 040338          262 NMISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY----TCYFVCMV  324 (385)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~a~~~~-------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~li  324 (385)
                      .+..-..|..+....|+..+|...|             ..-.+..+....++...|...++.+.+.++    +..--.+.
T Consensus        88 Tvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll~a  167 (251)
T COG4700          88 TVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLLFA  167 (251)
T ss_pred             hHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHHHH
Confidence            3444444555556666666665555             344455555667777777788877777666    55666677


Q ss_pred             HHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHhcCChHHHHH
Q 040338          325 DLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       325 ~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      ..|...|++.+|+.-|+....- |+...-.....-+.++|..+++..
T Consensus       168 R~laa~g~~a~Aesafe~a~~~ypg~~ar~~Y~e~La~qgr~~ea~a  214 (251)
T COG4700         168 RTLAAQGKYADAESAFEVAISYYPGPQARIYYAEMLAKQGRLREANA  214 (251)
T ss_pred             HHHHhcCCchhHHHHHHHHHHhCCCHHHHHHHHHHHHHhcchhHHHH
Confidence            7788888888888888777653 444433333333455665554443

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.01  E-value=0.42  Score=42.95  Aligned_cols=133  Identities=12%  Similarity=0.046  Sum_probs=98.2

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  166 (385)
                      ..+|...|+...+..-++.|..+|-+..+.+..                 .+++..++++|..++ .|++.-|.++|+.-
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~-----------------~h~vyi~~A~~E~~~-~~d~~ta~~ifelG  458 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIV-----------------GHHVYIYCAFIEYYA-TGDRATAYNIFELG  458 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCC-----------------CcceeeeHHHHHHHh-cCCcchHHHHHHHH
Confidence            456778888888888899999999998887743                 689999999998887 57788999999876


Q ss_pred             HHCCCCCCHhhH-HHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcC
Q 040338          167 WNHGFGLSSMLY-ATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEG  245 (385)
Q Consensus       167 ~~~g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~  245 (385)
                      ...  -||...| .--+..+.+.++-+.|..+|+..+.. +..+                    --...|..+|.--..-
T Consensus       459 l~~--f~d~~~y~~kyl~fLi~inde~naraLFetsv~r-~~~~--------------------q~k~iy~kmi~YEs~~  515 (660)
T COG5107         459 LLK--FPDSTLYKEKYLLFLIRINDEENARALFETSVER-LEKT--------------------QLKRIYDKMIEYESMV  515 (660)
T ss_pred             HHh--CCCchHHHHHHHHHHHHhCcHHHHHHHHHHhHHH-HHHh--------------------hhhHHHHHHHHHHHhh
Confidence            554  5666665 34566778899999999999965543 1111                    0123556677766777


Q ss_pred             CChhHHHHHHHhccc
Q 040338          246 GSTQKADLAFELMSR  260 (385)
Q Consensus       246 g~~~~A~~~~~~m~~  260 (385)
                      |++..+..+=+.|.+
T Consensus       516 G~lN~v~sLe~rf~e  530 (660)
T COG5107         516 GSLNNVYSLEERFRE  530 (660)
T ss_pred             cchHHHHhHHHHHHH
Confidence            788777777666654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.99  E-value=0.035  Score=36.63  Aligned_cols=56  Identities=16%  Similarity=0.062  Sum_probs=34.0

Q ss_pred             HHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338           95 DMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus        95 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      ..|.+.+++++|.++++++...+                   +.+...|.....++.+.|++++|...|+...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-------------------p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-------------------PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-------------------cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34556666666666666665544                   245555666666666666666666666666653

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.98  E-value=0.08  Score=43.26  Aligned_cols=177  Identities=12%  Similarity=-0.086  Sum_probs=99.7

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHCCCC-C-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          146 MISILTRHGFGFETLCTFIELWNHGFG-L-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       146 li~~~~~~~~~~~a~~~~~~m~~~g~~-p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      ....+.+.|++.+|...|+.+...-.. | -....-.+..++.+.|+++.|...++.+++.-+.....-+.-.+.+.+..
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~   90 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYY   90 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHH
Confidence            344567899999999999999875221 1 23345567888999999999999999999886654443343333332211


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHH---HHHHHHhcCCCCchHHHHHHHHHHHHhccc
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMV---LISAFSQAGVLEKPRFFFFFVSLLSGCSHS  298 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~---li~~~~~~g~~~~a~~~~~~~~l~~~~~~~  298 (385)
                      ..         +...+......+...+|...|+.+.+  |+..-...   .+..+ +..   -|.   .--.+..-|.+.
T Consensus        91 ~~---------~~~~~~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l-~~~---la~---~e~~ia~~Y~~~  154 (203)
T PF13525_consen   91 KQ---------IPGILRSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAEL-RNR---LAE---HELYIARFYYKR  154 (203)
T ss_dssp             HH---------HHHHH-TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHH-HHH---HHH---HHHHHHHHHHCT
T ss_pred             Hh---------CccchhcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHH-HHH---HHH---HHHHHHHHHHHc
Confidence            10         00000001222334566666666654  33211100   00000 000   000   112355668888


Q ss_pred             CChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHH
Q 040338          299 GPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKK  338 (385)
Q Consensus       299 ~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~  338 (385)
                      |.+..|..-++.+.+..+     ......++.+|.+.|..+.|..
T Consensus       155 ~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~~  199 (203)
T PF13525_consen  155 GKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAADT  199 (203)
T ss_dssp             T-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHHH
Confidence            999999999999988877     5666778999999998885543

>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=95.96  E-value=0.025  Score=43.44  Aligned_cols=71  Identities=11%  Similarity=-0.087  Sum_probs=53.4

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHH-----hCCCCchHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVH-----MEPSLDVFVG  213 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  213 (385)
                      +...++..+...|++++|..+.+.+... -+.|...|..+|.++...|+...|.++|+.+.+     .|+.|+..+-
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~-dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALAL-DPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH-STT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            4555677788899999999999999885 244888999999999999999999999998864     4888877654

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.93  E-value=0.18  Score=43.75  Aligned_cols=131  Identities=9%  Similarity=0.059  Sum_probs=88.9

Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh--c----CChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK--C----GAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD  139 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~--~----g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~  139 (385)
                      ..+++...+++.|++.|+.-+..+|-+..-....  .    ....+|.++|+.|++.-++               +..++
T Consensus        76 ~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~f---------------LTs~~  140 (297)
T PF13170_consen   76 EAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPF---------------LTSPE  140 (297)
T ss_pred             HHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCcc---------------ccCcc
Confidence            3467788999999999999888777664444333  2    2456788999999876431               11466


Q ss_pred             cchHHHHHHHHHhCCCc----hHHHHHHHHHHHCCCCCC-H-hhHHHHHHHhcCccC--ccchhhHHHHHHHhCCCCchH
Q 040338          140 LVSWNTMISILTRHGFG----FETLCTFIELWNHGFGLS-S-MLYATAFSARASVYD--LEWGPHLHSRVVHMEPSLDVF  211 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~----~~a~~~~~~m~~~g~~p~-~-~t~~~ll~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~  211 (385)
                      -.++..|+..  ..+++    +.+..+|+.+.+.|+..+ . ...+.++..+....+  ...+.++++.+.+.|+++...
T Consensus       141 D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~  218 (297)
T PF13170_consen  141 DYPFAALLAM--TSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYM  218 (297)
T ss_pred             chhHHHHHhc--ccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccc
Confidence            6777777655  33333    467788999999897763 3 344445544433333  347888999999999987776


Q ss_pred             HH
Q 040338          212 VG  213 (385)
Q Consensus       212 ~~  213 (385)
                      .|
T Consensus       219 ~y  220 (297)
T PF13170_consen  219 HY  220 (297)
T ss_pred             cc
Confidence            66

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.83  E-value=0.1  Score=47.11  Aligned_cols=114  Identities=11%  Similarity=-0.091  Sum_probs=79.9

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH----hhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS----MLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVG  213 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  213 (385)
                      .+...|+.+..+|...|++++|+..|++..+.  .|+.    .+|..+..+|...|+.++|++.++..++.+.    ..|
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALelsn----~~f  146 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDYN----LKF  146 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcc----hhH
Confidence            35678999999999999999999999998874  6764    4689999999999999999999999988621    112


Q ss_pred             HHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC-----hhHHHHHHHhcccC
Q 040338          214 SGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS-----TQKADLAFELMSRR  261 (385)
Q Consensus       214 ~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~-----~~~A~~~~~~m~~~  261 (385)
                      .    .+.+..+++.-.+...+..++....+.|.     ...-.++..+.+.|
T Consensus       147 ~----~i~~DpdL~plR~~pef~eLlee~rk~G~~~g~~~~~~~kL~~E~~aP  195 (453)
T PLN03098        147 S----TILNDPDLAPFRASPEFKELQEEARKGGEDIGSSFRRDLKLISEVQAP  195 (453)
T ss_pred             H----HHHhCcchhhhcccHHHHHHHHHHHHhCCccCCchhhHHHHHHHHhch
Confidence            1    12222222222344567777777777764     33344555555554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.80  E-value=0.17  Score=43.02  Aligned_cols=100  Identities=13%  Similarity=-0.002  Sum_probs=70.4

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC--chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD--ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      .|+..+..+..   .|++++|...|+.+.+......  ...+-.+..+|...|++++|...|+.+.+..+.         
T Consensus       145 ~Y~~A~~l~~~---~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~---------  212 (263)
T PRK10803        145 DYNAAIALVQD---KSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPK---------  212 (263)
T ss_pred             HHHHHHHHHHh---cCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC---------
Confidence            45555544333   6899999999999998732211  257778888999999999999999888654320         


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                             .+.....+-.+...+...|++++|..+|+...+.
T Consensus       213 -------s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        213 -------SPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             -------CcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence                   0122334445566777889999999999988775

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=95.79  E-value=0.094  Score=46.29  Aligned_cols=257  Identities=13%  Similarity=-0.072  Sum_probs=137.5

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCc----hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC
Q 040338           64 CVGNIKMALHLHGLVKKFYFVSDE----SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD  139 (385)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~  139 (385)
                      +.|+.+..+.+|+..++.|.. |.    .+|..|-++|.-.+++++|++.-..    ++       .-|..+=++..+  
T Consensus        29 k~gdcraGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH~h----Dl-------tlar~lgdklGE--   94 (639)
T KOG1130|consen   29 KMGDCRAGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYHTH----DL-------TLARLLGDKLGE--   94 (639)
T ss_pred             hccchhhhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhhhh----hH-------HHHHHhcchhcc--
Confidence            389999999999999998853 43    3456666777777888888876321    00       000000011100  


Q ss_pred             cchHHHHHHHHHhCCCchHHHHHH----HHHHHCCC-CCCHhhHHHHHHHhcCccCc-------------cchhhHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTF----IELWNHGF-GLSSMLYATAFSARASVYDL-------------EWGPHLHSRV  201 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~----~~m~~~g~-~p~~~t~~~ll~~~~~~~~~-------------~~a~~~~~~~  201 (385)
                      ..+...|-+.+--.|.+++|+-+-    +-..+.|- ......+..+-+.|...|..             +++...++..
T Consensus        95 AKssgNLGNtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~A  174 (639)
T KOG1130|consen   95 AKSSGNLGNTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENA  174 (639)
T ss_pred             ccccccccchhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHH
Confidence            111122233333445555554322    11222221 11234444555555544431             1122222221


Q ss_pred             HHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---------CChhhHHHHHHH
Q 040338          202 VHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---------RNMISWMVLISA  272 (385)
Q Consensus       202 ~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---------~~~~~~~~li~~  272 (385)
                      .+        .|-.=+..-.+.|+..  .--..|..|.+.|.-.|+++.|+..-+.=..         ..-..+..|..+
T Consensus       175 v~--------fy~eNL~l~~~lgDr~--aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~  244 (639)
T KOG1130|consen  175 VK--------FYMENLELSEKLGDRL--AQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNC  244 (639)
T ss_pred             HH--------HHHHHHHHHHHhhhHH--hhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchh
Confidence            11        1111111111111100  0112445555666677888888766543221         123567778888


Q ss_pred             HHhcCCCCchHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHH
Q 040338          273 FSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDL  326 (385)
Q Consensus       273 ~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~  326 (385)
                      ++-.|+++.|.+.|                  +.-++..+|.-..++++|+..+.+-...-.        ...+-+|..+
T Consensus       245 hiflg~fe~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna  324 (639)
T KOG1130|consen  245 HIFLGNFELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNA  324 (639)
T ss_pred             hhhhcccHhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            88888888888888                  344555666666778888887776443211        6677788999


Q ss_pred             HHccCCHHHHHHHHHhCC
Q 040338          327 LGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       327 ~~~~g~~~~A~~~~~~m~  344 (385)
                      |...|..+.|+.+.+.-.
T Consensus       325 ~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  325 FNALGEHRKALYFAELHL  342 (639)
T ss_pred             HHhhhhHHHHHHHHHHHH
Confidence            999999888888776543

>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=95.62  E-value=0.6  Score=34.49  Aligned_cols=138  Identities=11%  Similarity=-0.001  Sum_probs=80.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|.+++..++..+...+   .+..-||.+|--....-+-+...++++.+-+.--.+.-|++.....-+..+. .+..-.+
T Consensus        15 dG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n-~~se~vD   90 (161)
T PF09205_consen   15 DGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRN-KLSEYVD   90 (161)
T ss_dssp             TT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT----HHHH
T ss_pred             hchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhc-chHHHHH
Confidence            47777777777777664   3455566666555555555555555555533221111133333332222221 2334456


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                      ..+......|+-+.-.+++.++.+. -.|+......+..+|.+.|+..++.+++.+.-+.|++
T Consensus        91 ~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   91 LALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            7788889999999999999988753 4677777888999999999999999999999998863

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>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=95.57  E-value=0.19  Score=36.99  Aligned_cols=133  Identities=16%  Similarity=0.100  Sum_probs=75.8

Q ss_pred             CCChhHHHHHHHhccc-CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHh--cccCChhhHHHHHHHHHhccc-hhhH
Q 040338          245 GGSTQKADLAFELMSR-RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGC--SHSGPVTKGKHYFTAMAKFTY-TCYF  320 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~-~~~~  320 (385)
                      .|.+++..++..+... .+..-||-+|--....-+-+-..+++  ..+...+  ...|++......+   ...+. ....
T Consensus        15 dG~V~qGveii~k~v~Ssni~E~NWvICNiiDaa~C~yvv~~L--dsIGkiFDis~C~NlKrVi~C~---~~~n~~se~v   89 (161)
T PF09205_consen   15 DGDVKQGVEIIEKTVNSSNIKEYNWVICNIIDAADCDYVVETL--DSIGKIFDISKCGNLKRVIECY---AKRNKLSEYV   89 (161)
T ss_dssp             TT-HHHHHHHHHHHHHHS-HHHHTHHHHHHHHH--HHHHHHHH--HHHGGGS-GGG-S-THHHHHHH---HHTT---HHH
T ss_pred             hchHHHHHHHHHHHcCcCCccccceeeeecchhhchhHHHHHH--HHHhhhcCchhhcchHHHHHHH---HHhcchHHHH
Confidence            4677777888877765 34444444443332222211111111  1111110  1223333322222   22233 6677


Q ss_pred             HHHHHHHHccCCHHHHHHHHHhCCC--CCCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          321 VCMVDLLGLSGLLGEAKKLIDEMPS--KPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       321 ~~li~~~~~~g~~~~A~~~~~~m~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..-+..+..+|+-+...+++.++..  ++++...-.+..||.+.|+..++.+++++..+.|++.
T Consensus        90 D~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~kE  153 (161)
T PF09205_consen   90 DLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLKE  153 (161)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchHH
Confidence            7788899999999999999999863  4788888889999999999999999999999998764

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.56  E-value=0.66  Score=35.20  Aligned_cols=86  Identities=6%  Similarity=-0.053  Sum_probs=48.9

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      ...++..+.+.+.......+++.+.+.+                   ..+...+|.++..|++.+ ..+.++.++.    
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~-------------------~~~~~~~~~li~ly~~~~-~~~ll~~l~~----   65 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLN-------------------SENPALQTKLIELYAKYD-PQKEIERLDN----   65 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccC-------------------ccchhHHHHHHHHHHHHC-HHHHHHHHHh----
Confidence            3456666666667777777777665554                   245556777777777653 3344444432    


Q ss_pred             CCCCCHhhHHHHHHHhcCccCccchhhHHHHH
Q 040338          170 GFGLSSMLYATAFSARASVYDLEWGPHLHSRV  201 (385)
Q Consensus       170 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  201 (385)
                        .++......+++.|.+.+.++++.-++..+
T Consensus        66 --~~~~yd~~~~~~~c~~~~l~~~~~~l~~k~   95 (140)
T smart00299       66 --KSNHYDIEKVGKLCEKAKLYEEAVELYKKD   95 (140)
T ss_pred             --ccccCCHHHHHHHHHHcCcHHHHHHHHHhh
Confidence              123333344666666666666665555544

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.51  E-value=0.77  Score=34.81  Aligned_cols=129  Identities=6%  Similarity=-0.036  Sum_probs=83.5

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ......+|..+..   .+.+.....+++.+...| ..+...++.++..|++.. .++..+.+..                
T Consensus         7 ~~~~~~vv~~~~~---~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~----------------   65 (140)
T smart00299        7 PIDVSEVVELFEK---RNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN----------------   65 (140)
T ss_pred             cCCHHHHHHHHHh---CCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh----------------
Confidence            3345677888766   789999999999999887 468889999999999864 3444555542                


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCc-cCccchhhHHHHHHHhCCC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASV-YDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~  207 (385)
                              ..+......++..|.+.+.++++.-++.++...     .    ..+..+... ++.+.|.++...-      
T Consensus        66 --------~~~~yd~~~~~~~c~~~~l~~~~~~l~~k~~~~-----~----~Al~~~l~~~~d~~~a~~~~~~~------  122 (140)
T smart00299       66 --------KSNHYDIEKVGKLCEKAKLYEEAVELYKKDGNF-----K----DAIVTLIEHLGNYEKAIEYFVKQ------  122 (140)
T ss_pred             --------ccccCCHHHHHHHHHHcCcHHHHHHHHHhhcCH-----H----HHHHHHHHcccCHHHHHHHHHhC------
Confidence                    123334455777788888888888888776321     1    122222222 6777777766641      


Q ss_pred             CchHHHHHHHHHHH
Q 040338          208 LDVFVGSGLIDMYL  221 (385)
Q Consensus       208 ~~~~~~~~li~~~~  221 (385)
                      .+...|..++..+.
T Consensus       123 ~~~~lw~~~~~~~l  136 (140)
T smart00299      123 NNPELWAEVLKALL  136 (140)
T ss_pred             CCHHHHHHHHHHHH
Confidence            24556655555443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.47  E-value=2.6  Score=40.58  Aligned_cols=101  Identities=13%  Similarity=0.035  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHhcCCCCchHHHH---------HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHH
Q 040338          265 SWMVLISAFSQAGVLEKPRFFF---------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGE  335 (385)
Q Consensus       265 ~~~~li~~~~~~g~~~~a~~~~---------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  335 (385)
                      +.+--+.-+...|+..+|.++-         .|-.-+.+++..++|++..++-+..+.   +.-|.-++.+|.+.|+.++
T Consensus       686 Sl~dTv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskks---PIGy~PFVe~c~~~~n~~E  762 (829)
T KOG2280|consen  686 SLHDTVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKKS---PIGYLPFVEACLKQGNKDE  762 (829)
T ss_pred             cHHHHHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccCC---CCCchhHHHHHHhcccHHH
Confidence            4455566677888888888877         677778888888998877766555443   6667778899999999999


Q ss_pred             HHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          336 AKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       336 A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      |.+.+-+....+      -...+|.+.|++.+|.++.-+
T Consensus       763 A~KYiprv~~l~------ekv~ay~~~~~~~eAad~A~~  795 (829)
T KOG2280|consen  763 AKKYIPRVGGLQ------EKVKAYLRVGDVKEAADLAAE  795 (829)
T ss_pred             HhhhhhccCChH------HHHHHHHHhccHHHHHHHHHH
Confidence            999987766432      577888888888888776544

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.30  E-value=0.2  Score=42.45  Aligned_cols=111  Identities=14%  Similarity=-0.002  Sum_probs=73.9

Q ss_pred             CchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHH
Q 040338          229 ESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGK  305 (385)
Q Consensus       229 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~  305 (385)
                      +.|...|-.|...|...|+.+.|..-|..-.+   +|...+..+..++....+                   ..+-.++.
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~-------------------~~~ta~a~  213 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAG-------------------QQMTAKAR  213 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcC-------------------CcccHHHH
Confidence            45677777777777777777777777766654   355555555555433321                   12345677


Q ss_pred             HHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHH
Q 040338          306 HYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGA  358 (385)
Q Consensus       306 ~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~  358 (385)
                      .+|+++.+..+  .....-|...+...|++.+|...++.|.+. |....+..+|..
T Consensus       214 ~ll~~al~~D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie~  269 (287)
T COG4235         214 ALLRQALALDPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIER  269 (287)
T ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHHH
Confidence            78888887777  666666777778888888888888888775 555566666543

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.20  E-value=1.1  Score=37.46  Aligned_cols=123  Identities=12%  Similarity=0.061  Sum_probs=84.6

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|.+.-...++.+..+...+.++.....|.+.-.+.|+.+.|...|++..+...                  +.|..+++
T Consensus       190 ~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~------------------kL~~~q~~  251 (366)
T KOG2796|consen  190 MKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQ------------------KLDGLQGK  251 (366)
T ss_pred             chhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHh------------------hhhccchh
Confidence            688888999999999987777888888999999999999999999998765433                  33444444


Q ss_pred             HHH-----HHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          145 TMI-----SILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       145 ~li-----~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      .++     ..|.-++++..|...|++....+- -|....|.-.-+..=.|+..+|++.++.|+..-+
T Consensus       252 ~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~-~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P  317 (366)
T KOG2796|consen  252 IMVLMNSAFLHLGQNNFAEAHRFFTEILRMDP-RNAVANNNKALCLLYLGKLKDALKQLEAMVQQDP  317 (366)
T ss_pred             HHHHhhhhhheecccchHHHHHHHhhccccCC-CchhhhchHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            333     345556677777877877765421 1333333322233335777888888888877643

>PF14669 Asp_Glu_race_2: Putative aspartate racemase

Probab=95.09  E-value=0.9  Score=35.87  Aligned_cols=92  Identities=10%  Similarity=0.081  Sum_probs=70.9

Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH---HHHHHHHHhcccCChhhHHHHHHHHHhccc-----------
Q 040338          251 ADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF---FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----------  316 (385)
Q Consensus       251 A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------  316 (385)
                      |+.+.++-+++....|....++-++.-+.+++-+.+   .-.+++-.|.+.-+|.++.++++.|.+...           
T Consensus        95 a~~Ltkd~Kdk~~vPFceFAetV~k~~q~~e~dK~~LGRiGiS~m~~Yhk~~qW~KGrkvLd~l~el~i~ft~LKGL~g~  174 (233)
T PF14669_consen   95 AEALTKDSKDKPGVPFCEFAETVCKDPQNDEVDKTLLGRIGISLMYSYHKTLQWSKGRKVLDKLHELQIHFTSLKGLTGP  174 (233)
T ss_pred             HHHHHhcccccCCCCHHHHHHHHhcCCccchhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCccCc
Confidence            344444445556788999999999888888887777   666778888889999999999999887444           


Q ss_pred             ------hhhHHHHHHHHHccCCHHHHHHHHHh
Q 040338          317 ------TCYFVCMVDLLGLSGLLGEAKKLIDE  342 (385)
Q Consensus       317 ------~~~~~~li~~~~~~g~~~~A~~~~~~  342 (385)
                            -...|.-...+.++|.+|-|..++++
T Consensus       175 e~~asrCqivn~AaEiFL~sgsidGA~~vLre  206 (233)
T PF14669_consen  175 EKLASRCQIVNIAAEIFLKSGSIDGALWVLRE  206 (233)
T ss_pred             cccCchhhhHHHHHHHHHHcCCchHHHHHHhc
Confidence                  34556677788888999988888874

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.06  E-value=0.23  Score=42.13  Aligned_cols=119  Identities=11%  Similarity=-0.006  Sum_probs=84.2

Q ss_pred             ChhhHHHHHHHHHh--cCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC---CHH
Q 040338          262 NMISWMVLISAFSQ--AGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG---LLG  334 (385)
Q Consensus       262 ~~~~~~~li~~~~~--~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g---~~~  334 (385)
                      +..+.+.++..+-.  ..+++.+.   .|..|..+|...|+.+.|..-|....+.-.  +..+..+..++..+.   ...
T Consensus       134 ~~~~~~~l~a~Le~~L~~nP~d~e---gW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta  210 (287)
T COG4235         134 AEQEMEALIARLETHLQQNPGDAE---GWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTA  210 (287)
T ss_pred             CcccHHHHHHHHHHHHHhCCCCch---hHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccH
Confidence            33444444444322  22333333   556677777777777777888888777665  677777777665433   466


Q ss_pred             HHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          335 EAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       335 ~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ++..+|+++...  .|+.+-.-|...+...|++.+|...|+.|.+..|.+.
T Consensus       211 ~a~~ll~~al~~D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~  261 (287)
T COG4235         211 KARALLRQALALDPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADD  261 (287)
T ss_pred             HHHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCCC
Confidence            899999999874  4667777888899999999999999999999888754

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=94.74  E-value=0.88  Score=42.49  Aligned_cols=166  Identities=16%  Similarity=0.095  Sum_probs=94.7

Q ss_pred             HHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHH
Q 040338          160 LCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALV  239 (385)
Q Consensus       160 ~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li  239 (385)
                      .-+|.-+... ++|.   +..+++..+=.||-+.+++.+.+..+.+---.+.. .-++               -.|+.++
T Consensus       177 ~G~f~L~lSl-LPp~---~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la-~L~L---------------L~y~~~~  236 (468)
T PF10300_consen  177 FGLFNLVLSL-LPPK---VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLA-ALVL---------------LWYHLVV  236 (468)
T ss_pred             HHHHHHHHHh-CCHH---HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHH-HHHH---------------HHHHHHH
Confidence            3445555443 3443   33455666667888888888887665332111111 1111               1334444


Q ss_pred             HHHHc----CCChhHHHHHHHhccc--CChhhHHHHH-HHHHhcCCCCchHHHH----------------HHHHHHHHhc
Q 040338          240 TMYAE----GGSTQKADLAFELMSR--RNMISWMVLI-SAFSQAGVLEKPRFFF----------------FFVSLLSGCS  296 (385)
Q Consensus       240 ~~~~~----~g~~~~A~~~~~~m~~--~~~~~~~~li-~~~~~~g~~~~a~~~~----------------~~~~l~~~~~  296 (385)
                      ..+..    ..+.+.|.++++.+.+  |+...|.-.- ..+...|++++|++.+                .+--+.-.+.
T Consensus       237 ~~~~~~~~~~~~~~~a~~lL~~~~~~yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~  316 (468)
T PF10300_consen  237 PSFLGIDGEDVPLEEAEELLEEMLKRYPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHM  316 (468)
T ss_pred             HHHcCCcccCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHH
Confidence            44433    4567889999999987  7766665443 3455677777777777                4444555556


Q ss_pred             ccCChhhHHHHHHHHHhccc-hhhHHHH--HHHHHccCCH-------HHHHHHHHhCCC
Q 040338          297 HSGPVTKGKHYFTAMAKFTY-TCYFVCM--VDLLGLSGLL-------GEAKKLIDEMPS  345 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~-~~~~~~l--i~~~~~~g~~-------~~A~~~~~~m~~  345 (385)
                      -.++|++|...|..+.+... ...+-..  ..++...|+.       ++|.++|.+.+.
T Consensus       317 ~~~~w~~A~~~f~~L~~~s~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  317 FQHDWEEAAEYFLRLLKESKWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHchHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            66777777777777776655 2222222  2233445655       666676666543

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=94.73  E-value=3.2  Score=37.66  Aligned_cols=238  Identities=13%  Similarity=0.032  Sum_probs=125.3

Q ss_pred             ccCCChHHHHHHHHHHHHcccch-hhHHh--------------hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCC
Q 040338            5 GSLKSLPIARKIHAQLISTCLIS-SIFLQ--------------LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGN   67 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~~~-~~~~~--------------~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~   67 (385)
                      .+.|++.+++.+|..+....-.. ..+.-              +++..........  .| ...|-.+..++.. -+.+.
T Consensus        17 qkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~nld~Me~~l~~l~~~~~-~s~~l~LF~~L~~-Y~~k~   94 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNNLDLMEKQLMELRQQFG-KSAYLPLFKALVA-YKQKE   94 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhhHHHHHHHHHHHHHhcC-CchHHHHHHHHHH-HHhhh
Confidence            36688899999999988764222 22221              4444444444333  22 3445556555543 23688


Q ss_pred             hHHHHHHHHHHHHh--ccCC------------CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhc
Q 040338           68 IKMALHLHGLVKKF--YFVS------------DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQ  133 (385)
Q Consensus        68 ~~~a~~~~~~m~~~--g~~~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~  133 (385)
                      +++|.+.+..-.+.  +..|            |...=+..++++.+.|++.++..++++|...-.              .
T Consensus        95 ~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~ll--------------k  160 (549)
T PF07079_consen   95 YRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLL--------------K  160 (549)
T ss_pred             HHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHh--------------h
Confidence            88888888777665  3222            222335667888889999999999888753211              1


Q ss_pred             CCCCCCcchHHHHHHHHHhC--------CCchHHHHHHH-------HHHHC------CCCCCHhhHHHHHHHhc--CccC
Q 040338          134 KMPERDLVSWNTMISILTRH--------GFGFETLCTFI-------ELWNH------GFGLSSMLYATAFSARA--SVYD  190 (385)
Q Consensus       134 ~~~~~~~~~~~~li~~~~~~--------~~~~~a~~~~~-------~m~~~------g~~p~~~t~~~ll~~~~--~~~~  190 (385)
                      +=..-+..+||.++-.+.++        ...+-+.+.|+       +|...      .+.|-...+..++.-..  -...
T Consensus       161 rE~~w~~d~yd~~vlmlsrSYfLEl~e~~s~dl~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~  240 (549)
T PF07079_consen  161 RECEWNSDMYDRAVLMLSRSYFLELKESMSSDLYPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVPKER  240 (549)
T ss_pred             hhhcccHHHHHHHHHHHhHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCCHhh
Confidence            11136777888744333332        12222222222       22211      13343333333333222  1122


Q ss_pred             ccchhhHHHHHHHhCCCCchH-HHHHHHHHHHhcCCCC----------------CCchhhHHHHHHHHHHcCCChhHHHH
Q 040338          191 LEWGPHLHSRVVHMEPSLDVF-VGSGLIDMYLKCGCNG----------------IESSIQIGKALVTMYAEGGSTQKADL  253 (385)
Q Consensus       191 ~~~a~~~~~~~~~~~~~~~~~-~~~~li~~~~~~g~~~----------------~~~~~~~~~~li~~~~~~g~~~~A~~  253 (385)
                      ..--.++++.-.+.-+.|+.. +...|...+...+ .+                .+.-+.++..++....+.++...|.+
T Consensus       241 l~~~mq~l~~We~~yv~p~~~LVi~~L~~~f~~~~-e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q  319 (549)
T PF07079_consen  241 LPPLMQILENWENFYVHPNYDLVIEPLKQQFMSDP-EQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQ  319 (549)
T ss_pred             ccHHHHHHHHHHhhccCCchhHHHHHHHHHHhcCh-HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            333344444444444555432 2233333333311 11                22335567777778888888888888


Q ss_pred             HHHhcc
Q 040338          254 AFELMS  259 (385)
Q Consensus       254 ~~~~m~  259 (385)
                      .+..++
T Consensus       320 ~l~lL~  325 (549)
T PF07079_consen  320 YLALLK  325 (549)
T ss_pred             HHHHHH
Confidence            777654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>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=94.69  E-value=0.32  Score=44.75  Aligned_cols=156  Identities=14%  Similarity=-0.047  Sum_probs=95.6

Q ss_pred             HHHHhCCCchHHHHHHHHHHHCCCCC--CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 040338          148 SILTRHGFGFETLCTFIELWNHGFGL--SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGC  225 (385)
Q Consensus       148 ~~~~~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  225 (385)
                      ....-.++++++.++.+.=.   +.|  +..-...+++.+.+.|..+.|+++-.+-..                      
T Consensus       269 k~av~~~d~~~v~~~i~~~~---ll~~i~~~~~~~i~~fL~~~G~~e~AL~~~~D~~~----------------------  323 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASN---LLPNIPKDQGQSIARFLEKKGYPELALQFVTDPDH----------------------  323 (443)
T ss_dssp             HHHHHTT-HHH-----HHHH---TGGG--HHHHHHHHHHHHHTT-HHHHHHHSS-HHH----------------------
T ss_pred             HHHHHcCChhhhhhhhhhhh---hcccCChhHHHHHHHHHHHCCCHHHHHhhcCChHH----------------------
Confidence            44456788888777664111   111  234467788888888888888876554322                      


Q ss_pred             CCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCCh
Q 040338          226 NGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPV  301 (385)
Q Consensus       226 ~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~  301 (385)
                                  =.....++|+++.|.++-++..  +...|..|.+...+.|+++-|.+.+    -|..++-.|.-.|+.
T Consensus       324 ------------rFeLAl~lg~L~~A~~~a~~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d~~~L~lLy~~~g~~  389 (443)
T PF04053_consen  324 ------------RFELALQLGNLDIALEIAKELD--DPEKWKQLGDEALRQGNIELAEECYQKAKDFSGLLLLYSSTGDR  389 (443)
T ss_dssp             ------------HHHHHHHCT-HHHHHHHCCCCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT-HHHHHHHHHHCT-H
T ss_pred             ------------HhHHHHhcCCHHHHHHHHHhcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcCccccHHHHHHhCCH
Confidence                        1344557788888887766554  5568888888888888888888888    777788888888888


Q ss_pred             hhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          302 TKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       302 ~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      +...++.+.....|.   ++....++.-.|+.++..+++.+...
T Consensus       390 ~~L~kl~~~a~~~~~---~n~af~~~~~lgd~~~cv~lL~~~~~  430 (443)
T PF04053_consen  390 EKLSKLAKIAEERGD---INIAFQAALLLGDVEECVDLLIETGR  430 (443)
T ss_dssp             HHHHHHHHHHHHTT----HHHHHHHHHHHT-HHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHccC---HHHHHHHHHHcCCHHHHHHHHHHcCC
Confidence            877777777666544   44444455556777777777665543

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.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.69  E-value=0.29  Score=44.29  Aligned_cols=66  Identities=11%  Similarity=-0.089  Sum_probs=48.6

Q ss_pred             CCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCc---chHHHHHHHHHhCCCchHHHH
Q 040338           85 SDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDL---VSWNTMISILTRHGFGFETLC  161 (385)
Q Consensus        85 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~li~~~~~~~~~~~a~~  161 (385)
                      .+...++.+..+|.+.|++++|+..|++..+.++                   .+.   .+|..+..+|...|+.++|+.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~P-------------------d~aeA~~A~yNLAcaya~LGr~dEAla  133 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALELNP-------------------NPDEAQAAYYNKACCHAYREEGKKAAD  133 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-------------------CchHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            3556778888888888888888888877665542                   222   357778888888888888888


Q ss_pred             HHHHHHHC
Q 040338          162 TFIELWNH  169 (385)
Q Consensus       162 ~~~~m~~~  169 (385)
                      .+++..+.
T Consensus       134 ~LrrALel  141 (453)
T PLN03098        134 CLRTALRD  141 (453)
T ss_pred             HHHHHHHh
Confidence            88887764

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=94.67  E-value=0.055  Score=31.60  Aligned_cols=32  Identities=31%  Similarity=0.270  Sum_probs=20.1

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +|..+..+|...|++++|.++++++++..|.+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~   34 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDD   34 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence            34556666666666666666666666666654

>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=94.61  E-value=0.26  Score=45.35  Aligned_cols=130  Identities=12%  Similarity=-0.024  Sum_probs=79.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCC-CccccccchHHHHHHhcCCCCCCcchH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNP-SLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      +++++.+.+....-.--. ..+..-.+.++..+-+.|..+.|+++...-..+ +....-|+++.|.++.++..  +...|
T Consensus       274 ~~d~~~v~~~i~~~~ll~-~i~~~~~~~i~~fL~~~G~~e~AL~~~~D~~~rFeLAl~lg~L~~A~~~a~~~~--~~~~W  350 (443)
T PF04053_consen  274 RGDFEEVLRMIAASNLLP-NIPKDQGQSIARFLEKKGYPELALQFVTDPDHRFELALQLGNLDIALEIAKELD--DPEKW  350 (443)
T ss_dssp             TT-HHH-----HHHHTGG-G--HHHHHHHHHHHHHTT-HHHHHHHSS-HHHHHHHHHHCT-HHHHHHHCCCCS--THHHH
T ss_pred             cCChhhhhhhhhhhhhcc-cCChhHHHHHHHHHHHCCCHHHHHhhcCChHHHhHHHHhcCCHHHHHHHHHhcC--cHHHH
Confidence            688888766663111000 112455778888888888888888876443211 11122277888888887764  66689


Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      ..|.....+.|+++-|.+.|.+..+         |..|+-.|.-.|+.+.-.++.+.....|.
T Consensus       351 ~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~~~  404 (443)
T PF04053_consen  351 KQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEERGD  404 (443)
T ss_dssp             HHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHccC
Confidence            9999999999999999999988643         34555566667777777777766666553

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.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=94.44  E-value=1.5  Score=44.35  Aligned_cols=109  Identities=13%  Similarity=0.057  Sum_probs=70.7

Q ss_pred             CChhhHHHH----HHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHcc
Q 040338          261 RNMISWMVL----ISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLS  330 (385)
Q Consensus       261 ~~~~~~~~l----i~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~  330 (385)
                      ++...+...    ..-+...+.+++|.-.|    -....+.+|...|+|.+|..+..++.....  ..+-..|+.-+..+
T Consensus       933 ~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~GklekAl~a~~~~~dWr~~l~~a~ql~~~~de~~~~a~~L~s~L~e~ 1012 (1265)
T KOG1920|consen  933 PDSEKQKVIYEAYADHLREELMSDEAALMYERCGKLEKALKAYKECGDWREALSLAAQLSEGKDELVILAEELVSRLVEQ 1012 (1265)
T ss_pred             cCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccHHHHHHHHHHhccHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHc
Confidence            455444444    44445567777777666    555667888888888888888887655444  44446688888888


Q ss_pred             CCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          331 GLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       331 g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      ++.-+|-++..+...+|.     ..+.-|++...+++|.++...
T Consensus      1013 ~kh~eAa~il~e~~sd~~-----~av~ll~ka~~~~eAlrva~~ 1051 (1265)
T KOG1920|consen 1013 RKHYEAAKILLEYLSDPE-----EAVALLCKAKEWEEALRVASK 1051 (1265)
T ss_pred             ccchhHHHHHHHHhcCHH-----HHHHHHhhHhHHHHHHHHHHh
Confidence            988888888888776432     233444555555555555433

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=94.33  E-value=0.76  Score=42.90  Aligned_cols=153  Identities=12%  Similarity=0.013  Sum_probs=99.2

Q ss_pred             hhhhHHHHHhhhC-CCCh---------hhHHHHHHHHHhhh-ccCChHHHHHHHHHHHHhccCCCchHHHhHH-HHHHhc
Q 040338           33 LIDDDYRVFCDIG-PRYL---------FTYNTMINGGVRCL-CVGNIKMALHLHGLVKKFYFVSDESIAKSSI-DMHVKC  100 (385)
Q Consensus        33 ~~~~A~~~~~~~~-~~~~---------~~~~~li~~~~~~~-~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li-~~~~~~  100 (385)
                      +-+.+.+.+..-. .++.         ..|+.++..++... .....+.|.++++.+.++  -|+...|.-.- +.+...
T Consensus       203 dR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lfl~~~gR~~~~~  280 (468)
T PF10300_consen  203 DRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALFLFFEGRLERLK  280 (468)
T ss_pred             cHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHh
Confidence            5555555555433 2222         35777776664421 256889999999999986  56776665544 566678


Q ss_pred             CChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHH
Q 040338          101 GAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYAT  180 (385)
Q Consensus       101 g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~  180 (385)
                      |++++|++.|++.....               .++++.....+--+...+.-..+|++|.+.|..+.+.. .-...+|..
T Consensus       281 g~~~~Ai~~~~~a~~~q---------------~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y  344 (468)
T PF10300_consen  281 GNLEEAIESFERAIESQ---------------SEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAY  344 (468)
T ss_pred             cCHHHHHHHHHHhccch---------------hhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHH
Confidence            99999999998765321               11222333445556667888899999999999998752 334556665


Q ss_pred             HHHH-hcCccCc-------cchhhHHHHHHH
Q 040338          181 AFSA-RASVYDL-------EWGPHLHSRVVH  203 (385)
Q Consensus       181 ll~~-~~~~~~~-------~~a~~~~~~~~~  203 (385)
                      +.-+ +...++.       ++|.+++.+...
T Consensus       345 ~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  345 LAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            5444 3456666       677777776543

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.32  E-value=2.3  Score=35.20  Aligned_cols=197  Identities=11%  Similarity=0.043  Sum_probs=97.2

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      ..|.-...+|-...++++|...+.+..+. .+-|...|..       .+.++.|.-+.+++.+.  .--...|+.-...|
T Consensus        32 s~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfhA-------AKayEqaamLake~~kl--sEvvdl~eKAs~lY  101 (308)
T KOG1585|consen   32 SLYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFHA-------AKAYEQAAMLAKELSKL--SEVVDLYEKASELY  101 (308)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHHH-------HHHHHHHHHHHHHHHHh--HHHHHHHHHHHHHH
Confidence            34555667888889999998888776531 2223222221       12334444444444332  11222333334444


Q ss_pred             HhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc------CC--hhhHHHHHHHHHhcCCCCchHHHHHHHHHH
Q 040338          221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR------RN--MISWMVLISAFSQAGVLEKPRFFFFFVSLL  292 (385)
Q Consensus       221 ~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~------~~--~~~~~~li~~~~~~g~~~~a~~~~~~~~l~  292 (385)
                      ..+                      |..+-|-..+++.-+      |+  +..|..-+...-..++...|.+++  ...-
T Consensus       102 ~E~----------------------GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~el~--gk~s  157 (308)
T KOG1585|consen  102 VEC----------------------GSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAFELY--GKCS  157 (308)
T ss_pred             HHh----------------------CCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHHHHH--HHhh
Confidence            444                      444444333332211      11  123333333344444444443332  3333


Q ss_pred             HHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCC------CCCcchHHHHHHH
Q 040338          293 SGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS------KPTCVIWGALLGA  358 (385)
Q Consensus       293 ~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~------~p~~~~~~~li~~  358 (385)
                      ..+.+...+++|-..+.+-.....        -..|-+.|-.+.-..++..|.+.++.--.      .-+..+...|+.+
T Consensus       158 r~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~a  237 (308)
T KOG1585|consen  158 RVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTA  237 (308)
T ss_pred             hHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHH
Confidence            334444455554444333222111        23355556666777788888888877322      1356677788888


Q ss_pred             HHhcCChHHHHHHH
Q 040338          359 CCSHYNTKLAELVM  372 (385)
Q Consensus       359 ~~~~g~~~~a~~~~  372 (385)
                      |- .||.+++..++
T Consensus       238 yd-~gD~E~~~kvl  250 (308)
T KOG1585|consen  238 YD-EGDIEEIKKVL  250 (308)
T ss_pred             hc-cCCHHHHHHHH
Confidence            76 46666665544

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=94.24  E-value=3.3  Score=38.12  Aligned_cols=92  Identities=11%  Similarity=0.049  Sum_probs=64.5

Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCc--chHHHHHHHHHhcC
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTC--VIWGALLGACCSHY  363 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~--~~~~~li~~~~~~g  363 (385)
                      ..++-+.|+.++|++.+.++.+..+    ..+...|+++|...+++.++..++.+-.+-  |..  .+|+..+-.....+
T Consensus       266 AmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaRav~  345 (539)
T PF04184_consen  266 AMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKARAVG  345 (539)
T ss_pred             HHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHHhhc
Confidence            3444567888888888888877554    556677999999999999999999888652  443  35776554444444


Q ss_pred             Ch---------------HHHHHHHHHHHhccccCC
Q 040338          364 NT---------------KLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       364 ~~---------------~~a~~~~~~~~~~~~~~~  383 (385)
                      +.               ..|.+.+.+..+.+|..+
T Consensus       346 d~fs~e~a~rRGls~ae~~aveAi~RAvefNPHVp  380 (539)
T PF04184_consen  346 DKFSPEAASRRGLSPAEMNAVEAIHRAVEFNPHVP  380 (539)
T ss_pred             cccCchhhhhcCCChhHHHHHHHHHHHHHhCCCCc
Confidence            31               245677788778877654

The molecular function of this protein is uncertain.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=94.20  E-value=2.9  Score=34.96  Aligned_cols=82  Identities=12%  Similarity=-0.042  Sum_probs=61.7

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCC-CCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHG-FGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLID  218 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  218 (385)
                      ..|+--+. -.+.|++++|.+.|+.+...- ..| ...+.-.++-++-+.++++.|+..+++..+..+.....-|-..|.
T Consensus        36 ~LY~~g~~-~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~Ylk  114 (254)
T COG4105          36 ELYNEGLT-ELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLK  114 (254)
T ss_pred             HHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHH
Confidence            34554444 357899999999999998653 122 456666778889999999999999999999887766667766666


Q ss_pred             HHHhc
Q 040338          219 MYLKC  223 (385)
Q Consensus       219 ~~~~~  223 (385)
                      +++..
T Consensus       115 gLs~~  119 (254)
T COG4105         115 GLSYF  119 (254)
T ss_pred             HHHHh
Confidence            66543

>PRK15331 chaperone protein SicA; Provisional

Probab=94.18  E-value=0.26  Score=38.09  Aligned_cols=79  Identities=13%  Similarity=0.155  Sum_probs=46.8

Q ss_pred             HHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHH
Q 040338          270 ISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGE  335 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~  335 (385)
                      .--+...|++++|..+|            -+..|..+|...+++++|...|........  +..+-....+|...|+.+.
T Consensus        44 Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~~  123 (165)
T PRK15331         44 AYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAK  123 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHH
Confidence            33445677777777776            344445555556667777776666554444  3333345666666777777


Q ss_pred             HHHHHHhCCCCCC
Q 040338          336 AKKLIDEMPSKPT  348 (385)
Q Consensus       336 A~~~~~~m~~~p~  348 (385)
                      |+.-|+...++|.
T Consensus       124 A~~~f~~a~~~~~  136 (165)
T PRK15331        124 ARQCFELVNERTE  136 (165)
T ss_pred             HHHHHHHHHhCcc
Confidence            7776666655433

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=94.18  E-value=0.074  Score=29.47  Aligned_cols=28  Identities=14%  Similarity=-0.071  Sum_probs=21.1

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhc
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                      +|..|.+.|.+.|++++|++++++.+..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~l   28 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALAL   28 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4677888888888888888888885543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.18  E-value=0.32  Score=40.74  Aligned_cols=87  Identities=15%  Similarity=0.026  Sum_probs=61.8

Q ss_pred             ccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC----cchHHHHHHHHHhcCChH
Q 040338          297 HSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT----CVIWGALLGACCSHYNTK  366 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~----~~~~~~li~~~~~~g~~~  366 (385)
                      +.|++..|.+-|....+..+     +..+-=|.+++...|++++|..+|..+.+. |+    ..+.--|.....+.|+.+
T Consensus       153 ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d  232 (262)
T COG1729         153 KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTD  232 (262)
T ss_pred             HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHH
Confidence            45667788888888877777     444445788888888888888888777653 22    234555666777788888


Q ss_pred             HHHHHHHHHHhccccCC
Q 040338          367 LAELVMRNLLQLDVKVF  383 (385)
Q Consensus       367 ~a~~~~~~~~~~~~~~~  383 (385)
                      +|...|+++.+.-|..+
T Consensus       233 ~A~atl~qv~k~YP~t~  249 (262)
T COG1729         233 EACATLQQVIKRYPGTD  249 (262)
T ss_pred             HHHHHHHHHHHHCCCCH
Confidence            88888888887776544

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.17  E-value=0.63  Score=38.80  Aligned_cols=129  Identities=10%  Similarity=0.005  Sum_probs=79.6

Q ss_pred             hHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCC
Q 040338           92 SSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGF  171 (385)
Q Consensus        92 ~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  171 (385)
                      .++..+--.|.+.-....+++..+.+.                  +.++..-..|.+.-.+.|+.+.|...|+...+..-
T Consensus       182 ~~~~~llG~kEy~iS~d~~~~vi~~~~------------------e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~  243 (366)
T KOG2796|consen  182 SMANCLLGMKEYVLSVDAYHSVIKYYP------------------EQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQ  243 (366)
T ss_pred             HHHHHHhcchhhhhhHHHHHHHHHhCC------------------cccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHh
Confidence            333444444555666666766666554                  55677777788888888888888888887765444


Q ss_pred             CCCHhhHHHHH-----HHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCC
Q 040338          172 GLSSMLYATAF-----SARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGG  246 (385)
Q Consensus       172 ~p~~~t~~~ll-----~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g  246 (385)
                      +.|..+++.++     ..+.-++++..|...+.++......                       +...-|+-.-+..-.|
T Consensus       244 kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~-----------------------~~~a~NnKALcllYlg  300 (366)
T KOG2796|consen  244 KLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPR-----------------------NAVANNNKALCLLYLG  300 (366)
T ss_pred             hhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCCC-----------------------chhhhchHHHHHHHHH
Confidence            44444444433     3355566777777777777655432                       1122232223333456


Q ss_pred             ChhHHHHHHHhcccC
Q 040338          247 STQKADLAFELMSRR  261 (385)
Q Consensus       247 ~~~~A~~~~~~m~~~  261 (385)
                      +..+|++.++.|.+.
T Consensus       301 ~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  301 KLKDALKQLEAMVQQ  315 (366)
T ss_pred             HHHHHHHHHHHHhcc
Confidence            888999999999873

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=94.07  E-value=2.4  Score=33.57  Aligned_cols=103  Identities=10%  Similarity=-0.018  Sum_probs=65.6

Q ss_pred             CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           47 RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        47 ~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                      |++..--.|-.++..   .|+..+|...|++....-+.-|....-.+.++....++...|...++.+-+-++.       
T Consensus        87 pTvqnr~rLa~al~e---lGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa-------  156 (251)
T COG4700          87 PTVQNRYRLANALAE---LGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPA-------  156 (251)
T ss_pred             hhHHHHHHHHHHHHH---hhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCc-------
Confidence            333333345555444   6777888887777766545556666666777777777777777777766443320       


Q ss_pred             HHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          127 RLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       127 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                                -.++.+.-.+...+...|++.+|..-|+.....
T Consensus       157 ----------~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~  189 (251)
T COG4700         157 ----------FRSPDGHLLFARTLAAQGKYADAESAFEVAISY  189 (251)
T ss_pred             ----------cCCCCchHHHHHHHHhcCCchhHHHHHHHHHHh
Confidence                      123334445566777778888888888777765

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=93.95  E-value=3.8  Score=35.39  Aligned_cols=176  Identities=13%  Similarity=0.024  Sum_probs=95.5

Q ss_pred             cCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhh
Q 040338          186 ASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMIS  265 (385)
Q Consensus       186 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~  265 (385)
                      .+.|+.+.|..++.+........++.....|.+.+              |+.-...+.+..+++.|...+++-.+     
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~--------------yn~G~~l~~~~~~~~~a~~wL~~a~~-----   64 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVC--------------YNIGKSLLSKKDKYEEAVKWLQRAYD-----   64 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHH--------------HHHHHHHHHcCCChHHHHHHHHHHHH-----
Confidence            35667777777777766644233333333343333              22223333333377777666654432     


Q ss_pred             HHHHHHHHHhc-CCCCchHHHH--HHHHHHHHhcccCCh---hhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHH
Q 040338          266 WMVLISAFSQA-GVLEKPRFFF--FFVSLLSGCSHSGPV---TKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAK  337 (385)
Q Consensus       266 ~~~li~~~~~~-g~~~~a~~~~--~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~  337 (385)
                         +++...+. ....+..++-  ++..++.+|...+..   ++|..+++.+....+  +.++-.-++.+.+.++.+++.
T Consensus        65 ---~l~~~~~~~~~~~~~~elr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~  141 (278)
T PF08631_consen   65 ---ILEKPGKMDKLSPDGSELRLSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYE  141 (278)
T ss_pred             ---HHHhhhhccccCCcHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHH
Confidence               00000111 1112221222  555555666555543   456666666655555  666666677777789999999


Q ss_pred             HHHHhCCCCC--CcchHHHHHHHHHh--cCChHHHHHHHHHHHhccccCC
Q 040338          338 KLIDEMPSKP--TCVIWGALLGACCS--HYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       338 ~~~~~m~~~p--~~~~~~~li~~~~~--~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +.+.+|....  ....+...++.+..  ......+...+++++-..+.|+
T Consensus       142 ~~L~~mi~~~~~~e~~~~~~l~~i~~l~~~~~~~a~~~ld~~l~~r~~~~  191 (278)
T PF08631_consen  142 EILMRMIRSVDHSESNFDSILHHIKQLAEKSPELAAFCLDYLLLNRFKSS  191 (278)
T ss_pred             HHHHHHHHhcccccchHHHHHHHHHHHHhhCcHHHHHHHHHHHHHHhCCC
Confidence            9999998763  34556666666522  2344567777777665555443

It is also involved in sporulation [].

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.90  E-value=3  Score=42.36  Aligned_cols=76  Identities=9%  Similarity=-0.078  Sum_probs=50.7

Q ss_pred             HHHHHHHcCCChhHHHHHHHhcccCChhhH---HHHHHHHHhcCCCCchHHHH-----HHHHHHHHhcccCChhhHHHHH
Q 040338          237 ALVTMYAEGGSTQKADLAFELMSRRNMISW---MVLISAFSQAGVLEKPRFFF-----FFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       237 ~li~~~~~~g~~~~A~~~~~~m~~~~~~~~---~~li~~~~~~g~~~~a~~~~-----~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      --+.+|..+|+|.+|..+-..+..+-....   ..|+.-+...+++-+|-++.     -..-.+..+++...+++|.++-
T Consensus       970 kAl~a~~~~~dWr~~l~~a~ql~~~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd~~~av~ll~ka~~~~eAlrva 1049 (1265)
T KOG1920|consen  970 KALKAYKECGDWREALSLAAQLSEGKDELVILAEELVSRLVEQRKHYEAAKILLEYLSDPEEAVALLCKAKEWEEALRVA 1049 (1265)
T ss_pred             HHHHHHHHhccHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcCHHHHHHHHhhHhHHHHHHHHH
Confidence            446677778888888888887766433222   56777888888888887766     4445555566666667666655


Q ss_pred             HHHH
Q 040338          309 TAMA  312 (385)
Q Consensus       309 ~~~~  312 (385)
                      ....
T Consensus      1050 ~~~~ 1053 (1265)
T KOG1920|consen 1050 SKAK 1053 (1265)
T ss_pred             Hhcc
Confidence            5444

>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=93.83  E-value=0.022  Score=43.60  Aligned_cols=54  Identities=11%  Similarity=-0.098  Sum_probs=34.6

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHH
Q 040338          146 MISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHS  199 (385)
Q Consensus       146 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  199 (385)
                      ++..+.+.+.++....+++.+...+..-+....+.++..|++.++.+...++++
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            455666677777777777777766555566667777777777766565555554

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.

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.76  E-value=2.9  Score=33.39  Aligned_cols=91  Identities=9%  Similarity=-0.030  Sum_probs=65.0

Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHhcCCh
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACCSHYNT  365 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~~g~~  365 (385)
                      ...+...+++++|...++.......     ...-.-|.......|.+|+|.+.++...+. -.......-...+...|+.
T Consensus        96 Ak~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w~~~~~elrGDill~kg~k  175 (207)
T COG2976          96 AKAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKEESWAAIVAELRGDILLAKGDK  175 (207)
T ss_pred             HHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccHHHHHHHHhhhHHHHcCch
Confidence            3455667778888888877664444     223334666778899999999999988764 1222233445679999999


Q ss_pred             HHHHHHHHHHHhccccC
Q 040338          366 KLAELVMRNLLQLDVKV  382 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~  382 (385)
                      ++|+.-|++.++.+..|
T Consensus       176 ~~Ar~ay~kAl~~~~s~  192 (207)
T COG2976         176 QEARAAYEKALESDASP  192 (207)
T ss_pred             HHHHHHHHHHHHccCCh
Confidence            99999999998887544

>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=93.71  E-value=1.6  Score=33.71  Aligned_cols=69  Identities=19%  Similarity=0.125  Sum_probs=41.3

Q ss_pred             HHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHh
Q 040338          293 SGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACCS  361 (385)
Q Consensus       293 ~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~  361 (385)
                      ..-...++.+.+..++..+.-.-+  ...-..-...+.+.|++++|..+|+++.+. |....-..|+..|..
T Consensus        18 ~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~CL~   89 (160)
T PF09613_consen   18 SVALRLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALCLY   89 (160)
T ss_pred             HHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHHHH
Confidence            333455677777777777776666  333333344456788888888888887765 333333344444433

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.61  E-value=1.5  Score=36.91  Aligned_cols=99  Identities=15%  Similarity=0.003  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccC--CCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFV--SDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      .|+.-+..+..    |++..|.+.|...++....  -....+-.|..++...|+.++|..+|..+.+..+.+        
T Consensus       144 ~Y~~A~~~~ks----gdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s--------  211 (262)
T COG1729         144 LYNAALDLYKS----GDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKS--------  211 (262)
T ss_pred             HHHHHHHHHHc----CCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCC--------
Confidence            37766665433    7777777777777775321  123455566777777777777777777665533200        


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                              +.-+...--|..+..+.|+.++|..+|++..+.
T Consensus       212 --------~KApdallKlg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         212 --------PKAPDALLKLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             --------CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence                    122334445556666777777777777777654

>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=93.55  E-value=0.06  Score=41.14  Aligned_cols=46  Identities=15%  Similarity=0.042  Sum_probs=36.6

Q ss_pred             HHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 040338          180 TAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGC  225 (385)
Q Consensus       180 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  225 (385)
                      .++..+.+.+.......+++.+...+...+....+.++..|++.+.
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~   57 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDP   57 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCC
Confidence            3677888889999999999999988877778888888888887764

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.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=93.49  E-value=4.5  Score=39.35  Aligned_cols=89  Identities=11%  Similarity=0.149  Sum_probs=51.2

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHH-HHHHccCC-----------HHHHHHHHHhCCCCC------
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMV-DLLGLSGL-----------LGEAKKLIDEMPSKP------  347 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li-~~~~~~g~-----------~~~A~~~~~~m~~~p------  347 (385)
                      .......-+...|++++|..+|....+... ....+.++ .+......           ...|.++.+.....+      
T Consensus       416 i~~~~A~~~e~~g~~~dAi~Ly~La~~~d~vl~lln~~Ls~~l~~~~~~~~~~s~~~~l~~la~~i~~~y~~~~~~~~~~  495 (613)
T PF04097_consen  416 IIEQAAREAEERGRFEDAILLYHLAEEYDKVLSLLNRLLSQVLSQPSSSSLSDSERERLIELAKEILERYKSNPHISSKV  495 (613)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCSSTSSSSSTTTTSHHHHHHHHHHHHTTSHHHHTTS
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCccccccccchhhhHHHHHHHHHHHHHhCcchHhhc
Confidence            444555556678888888888888776655 44444333 33333333           455666666665532      


Q ss_pred             ---CcchHHHHHHH-----HHhcCChHHHHHHHHHH
Q 040338          348 ---TCVIWGALLGA-----CCSHYNTKLAELVMRNL  375 (385)
Q Consensus       348 ---~~~~~~~li~~-----~~~~g~~~~a~~~~~~~  375 (385)
                         +..|+..|+..     +...|+++.|++.++++
T Consensus       496 ~~~~~~t~~~Ll~L~~ff~~~~~g~~~~AL~~i~~L  531 (613)
T PF04097_consen  496 SRKNRETFQLLLDLAEFFDLYHAGQYEQALDIIEKL  531 (613)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhC
Confidence               23355555433     46688999998777764

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=93.46  E-value=0.73  Score=39.27  Aligned_cols=78  Identities=13%  Similarity=0.142  Sum_probs=57.3

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      .++..++..+..+|+.+.+.+.+++....+                   +-+...|..+|.+|.+.|+...|+..|+.+.
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-------------------p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~  214 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-------------------PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLK  214 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-------------------ccchHHHHHHHHHHHHcCCchHHHHHHHHHH
Confidence            345556777777788888888877776655                   4677888888888888888888888888876


Q ss_pred             H-----CCCCCCHhhHHHHHHH
Q 040338          168 N-----HGFGLSSMLYATAFSA  184 (385)
Q Consensus       168 ~-----~g~~p~~~t~~~ll~~  184 (385)
                      +     .|+.|...+.......
T Consensus       215 ~~~~edlgi~P~~~~~~~y~~~  236 (280)
T COG3629         215 KTLAEELGIDPAPELRALYEEI  236 (280)
T ss_pred             HHhhhhcCCCccHHHHHHHHHH
Confidence            5     4777766665555444

>PRK15331 chaperone protein SicA; Provisional

Probab=93.36  E-value=1.3  Score=34.37  Aligned_cols=84  Identities=7%  Similarity=-0.089  Sum_probs=51.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|..+|.-+.-.++. +..-+..|..++-..+++++|...|......+                   ..|..++-
T Consensus        50 ~Gk~~eA~~~F~~L~~~d~~-n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-------------------~~dp~p~f  109 (165)
T PRK15331         50 QGRLDEAETFFRFLCIYDFY-NPDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-------------------KNDYRPVF  109 (165)
T ss_pred             CCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-------------------cCCCCccc
Confidence            47777777777777665433 44445555555556677777777775543222                   23334444


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      -.-.++...|+.+.|...|+...+
T Consensus       110 ~agqC~l~l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        110 FTGQCQLLMRKAAKARQCFELVNE  133 (165)
T ss_pred             hHHHHHHHhCCHHHHHHHHHHHHh
Confidence            456667777777777777776665

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.14  E-value=0.15  Score=27.63  Aligned_cols=32  Identities=19%  Similarity=0.007  Sum_probs=26.7

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          350 VIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       350 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      .+|..+..+|...|++++|+..+++.++.+|+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            46788888999999999999999999888875

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=93.02  E-value=0.61  Score=41.36  Aligned_cols=91  Identities=9%  Similarity=-0.072  Sum_probs=50.8

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHH-Hhc
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGAC-CSH  362 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~-~~~  362 (385)
                      ++.++.-+|.+.+++..|++.-+.....++  ....---..+|...|+++.|+..|+.+.+. |+-..-..=+..| .+.
T Consensus       259 ~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~  338 (397)
T KOG0543|consen  259 CHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQKI  338 (397)
T ss_pred             HhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHH
Confidence            666666666667777777666666666555  444444566666667777777777666653 5444333322222 222


Q ss_pred             CC-hHHHHHHHHHHHh
Q 040338          363 YN-TKLAELVMRNLLQ  377 (385)
Q Consensus       363 g~-~~~a~~~~~~~~~  377 (385)
                      .. .+...++|..|..
T Consensus       339 ~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  339 REYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            22 2334556666654

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.01  E-value=7.9  Score=38.03  Aligned_cols=175  Identities=9%  Similarity=-0.055  Sum_probs=94.0

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH----HHHHHHHhCCCchHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN----TMISILTRHGFGFETLCTFI  164 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~  164 (385)
                      ....-|+.+.+...++-|..+-+.-.                       .|..+-.    ...+.+.+.|++++|...|-
T Consensus       336 ~le~kL~iL~kK~ly~~Ai~LAk~~~-----------------------~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI  392 (933)
T KOG2114|consen  336 DLETKLDILFKKNLYKVAINLAKSQH-----------------------LDEDTLAEIHRKYGDYLYGKGDFDEATDQYI  392 (933)
T ss_pred             cHHHHHHHHHHhhhHHHHHHHHHhcC-----------------------CCHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            34556777777777777777764421                       2222222    23345567899999998887


Q ss_pred             HHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc
Q 040338          165 ELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE  244 (385)
Q Consensus       165 ~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~  244 (385)
                      +-... +.|.     .++.-|........-...++.+.+.|+.-. ..-                      ..|+.+|.+
T Consensus       393 ~tI~~-le~s-----~Vi~kfLdaq~IknLt~YLe~L~~~gla~~-dht----------------------tlLLncYiK  443 (933)
T KOG2114|consen  393 ETIGF-LEPS-----EVIKKFLDAQRIKNLTSYLEALHKKGLANS-DHT----------------------TLLLNCYIK  443 (933)
T ss_pred             HHccc-CChH-----HHHHHhcCHHHHHHHHHHHHHHHHcccccc-hhH----------------------HHHHHHHHH
Confidence            76543 4443     355566666666666777788888877432 222                      344555555


Q ss_pred             CCChhHHHHHHHhcccCChhh--HHHHHHHHHhcCCCCchHHHH-----HHHHHHHHhcccCChhhHHHHHHHHHhccc
Q 040338          245 GGSTQKADLAFELMSRRNMIS--WMVLISAFSQAGVLEKPRFFF-----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY  316 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~~~~~~--~~~li~~~~~~g~~~~a~~~~-----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  316 (385)
                      .++.++-.++.+...+ ....  ....+..+.+.+-.++|.-+-     .-..+--.+-..+++++|.+.++.+.-...
T Consensus       444 lkd~~kL~efI~~~~~-g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~he~vl~ille~~~ny~eAl~yi~slp~~e~  521 (933)
T KOG2114|consen  444 LKDVEKLTEFISKCDK-GEWFFDVETALEILRKSNYLDEAELLATKFKKHEWVLDILLEDLHNYEEALRYISSLPISEL  521 (933)
T ss_pred             hcchHHHHHHHhcCCC-cceeeeHHHHHHHHHHhChHHHHHHHHHHhccCHHHHHHHHHHhcCHHHHHHHHhcCCHHHH
Confidence            5555555555544431 1111  222334444444444443332     111222223456677777777766544433

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.95  E-value=4.8  Score=34.38  Aligned_cols=115  Identities=7%  Similarity=0.046  Sum_probs=78.0

Q ss_pred             hhhhHHHHHhhhC-----CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh-ccCCCchHHHhHHHHHHhcCChhHH
Q 040338           33 LIDDDYRVFCDIG-----PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF-YFVSDESIAKSSIDMHVKCGAVDYA  106 (385)
Q Consensus        33 ~~~~A~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~li~~~~~~g~~~~a  106 (385)
                      -+.+|.++|+...     -.|...-..+++....-. ........++.+.+... |-.++..+-..+|..+++.+++.+-
T Consensus       143 ~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~-~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl  221 (292)
T PF13929_consen  143 IVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDE-NTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKL  221 (292)
T ss_pred             HHHHHHHHhhccCcccceeeChHHHHHHHHHHHhcc-ccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHH
Confidence            6677888887432     234444455555544311 22555555666666543 4567888888999999999999999


Q ss_pred             HHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338          107 ESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus       107 ~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      .++++.-.....                 +..|...|..+|......|+..-..++.++
T Consensus       222 ~~fW~~~~~~~~-----------------~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  222 FQFWEQCIPNSV-----------------PGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHHHHhcccCC-----------------CCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            999987655421                 157888999999999999998665555544

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=92.82  E-value=7  Score=35.12  Aligned_cols=162  Identities=9%  Similarity=-0.071  Sum_probs=101.1

Q ss_pred             cchHHHHH-HHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHh--cCccCccchhhHHHHHHHhCCCCchH-HHHH
Q 040338          140 LVSWNTMI-SILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSAR--ASVYDLEWGPHLHSRVVHMEPSLDVF-VGSG  215 (385)
Q Consensus       140 ~~~~~~li-~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~  215 (385)
                      ..+|..|= .++...|++++|...-...++..  + ...+...+++.  .-..+.+.+...|++.++.++..... +-..
T Consensus       168 c~~a~~lka~cl~~~~~~~~a~~ea~~ilkld--~-~n~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~~~  244 (486)
T KOG0550|consen  168 CFKAKLLKAECLAFLGDYDEAQSEAIDILKLD--A-TNAEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSASM  244 (486)
T ss_pred             hhHHHHhhhhhhhhcccchhHHHHHHHHHhcc--c-chhHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhHhh
Confidence            34444332 45667788888887666655431  1 22334444443  34567778888888877765432111 1111


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-------CChhhHHHHHHHHHhcCCCCchHHHH--
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-------RNMISWMVLISAFSQAGVLEKPRFFF--  286 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~~~~~~~~li~~~~~~g~~~~a~~~~--  286 (385)
                      ..+.+            ..+..=.+...+.|++..|.+.|.+-..       ++...|.....+..+.|++.+|+.--  
T Consensus       245 ~~k~l------------e~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~  312 (486)
T KOG0550|consen  245 MPKKL------------EVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNE  312 (486)
T ss_pred             hHHHH------------HHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhh
Confidence            11111            2233344667789999999999998875       34556777778888999999988666  


Q ss_pred             ----------HHHHHHHHhcccCChhhHHHHHHHHHhccc
Q 040338          287 ----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY  316 (385)
Q Consensus       287 ----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  316 (385)
                                .|..-..++...++|++|.+-++...+...
T Consensus       313 Al~iD~syikall~ra~c~l~le~~e~AV~d~~~a~q~~~  352 (486)
T KOG0550|consen  313 ALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKAMQLEK  352 (486)
T ss_pred             hhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence                      455555566667888888888887766544

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.79  E-value=0.23  Score=26.72  Aligned_cols=32  Identities=25%  Similarity=0.110  Sum_probs=25.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .|..+...|...|++++|++.+++.++..|++
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~~   34 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALELDPNN   34 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHCcCC
Confidence            46677888889999999999999988887753

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=92.42  E-value=0.91  Score=34.25  Aligned_cols=87  Identities=13%  Similarity=-0.019  Sum_probs=59.3

Q ss_pred             cccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCc--chHHHHHHHHHhcC--C-
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTC--VIWGALLGACCSHY--N-  364 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~--~~~~~li~~~~~~g--~-  364 (385)
                      .+.|++++|.+.|+.+....+     ....-.++.+|.+.+++++|...+++..+- |+.  +-|-..+.++..-.  . 
T Consensus        21 l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~~~~~~  100 (142)
T PF13512_consen   21 LQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYYEQDEG  100 (142)
T ss_pred             HHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHHhhh
Confidence            467888888888888888777     556667888888899999988888888762 321  23444444433222  1 


Q ss_pred             --------------hHHHHHHHHHHHhccccC
Q 040338          365 --------------TKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       365 --------------~~~a~~~~~~~~~~~~~~  382 (385)
                                    ...|..-|+++++.-|+.
T Consensus       101 ~~~~~~~~drD~~~~~~A~~~f~~lv~~yP~S  132 (142)
T PF13512_consen  101 SLQSFFRSDRDPTPARQAFRDFEQLVRRYPNS  132 (142)
T ss_pred             HHhhhcccccCcHHHHHHHHHHHHHHHHCcCC
Confidence                          567777777777766653

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=92.39  E-value=1.2  Score=32.89  Aligned_cols=77  Identities=18%  Similarity=0.015  Sum_probs=58.1

Q ss_pred             HHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH----------------HHHHHHHHhcccCC
Q 040338          240 TMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF----------------FFVSLLSGCSHSGP  300 (385)
Q Consensus       240 ~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~----------------~~~~l~~~~~~~~~  300 (385)
                      -+.+..|+++.|++.|.....   .....||.=..++.-+|+.++|++-+                +|..-...|...|+
T Consensus        51 valaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~  130 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGN  130 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCc
Confidence            466788999999999987765   46788888888888888888887666                55555555666677


Q ss_pred             hhhHHHHHHHHHhccc
Q 040338          301 VTKGKHYFTAMAKFTY  316 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~  316 (385)
                      -+.|..=|+...+.|.
T Consensus       131 dd~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  131 DDAARADFEAAAQLGS  146 (175)
T ss_pred             hHHHHHhHHHHHHhCC
Confidence            7777777777666665

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=92.33  E-value=7.9  Score=34.57  Aligned_cols=109  Identities=17%  Similarity=0.017  Sum_probs=73.4

Q ss_pred             CCChHHHHHHHHHHH---HcccchhhHHh---------hhhhHHHHHhhhCCCChhhHHHHHHHHH-hhhccCChHHHHH
Q 040338            7 LKSLPIARKIHAQLI---STCLISSIFLQ---------LIDDDYRVFCDIGPRYLFTYNTMINGGV-RCLCVGNIKMALH   73 (385)
Q Consensus         7 ~~~~~~a~~~~~~~~---~~~~~~~~~~~---------~~~~A~~~~~~~~~~~~~~~~~li~~~~-~~~~~~~~~~a~~   73 (385)
                      .||-..|+..-.+..   +..-.|-+.+-         +.++|++-|+.|.. |+-+--.-++++- ...+.|..+-|.+
T Consensus        97 AGda~lARkmt~~~~~llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~-dPEtRllGLRgLyleAqr~GareaAr~  175 (531)
T COG3898          97 AGDASLARKMTARASKLLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLD-DPETRLLGLRGLYLEAQRLGAREAARH  175 (531)
T ss_pred             cCchHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhc-ChHHHHHhHHHHHHHHHhcccHHHHHH
Confidence            577777776655543   33333333333         99999999999983 2222222333322 2344799999998


Q ss_pred             HHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCC
Q 040338           74 LHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPS  117 (385)
Q Consensus        74 ~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  117 (385)
                      .-+..-+.- +--...+...+...|..|+++.|+++++.-....
T Consensus       176 yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~  218 (531)
T COG3898         176 YAERAAEKA-PQLPWAARATLEARCAAGDWDGALKLVDAQRAAK  218 (531)
T ss_pred             HHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHH
Confidence            888776643 2245788999999999999999999998765433

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=92.33  E-value=6.8  Score=33.81  Aligned_cols=152  Identities=11%  Similarity=0.084  Sum_probs=88.3

Q ss_pred             ccccCCChHHHHHHHHHHHHcc--cchhhHHh---------------h---------hhhHHHHHhh---hC--CCCh--
Q 040338            3 ACGSLKSLPIARKIHAQLISTC--LISSIFLQ---------------L---------IDDDYRVFCD---IG--PRYL--   49 (385)
Q Consensus         3 ~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~---------------~---------~~~A~~~~~~---~~--~~~~--   49 (385)
                      ...+.||++.|+..++++....  ..|+....               +         ++.|..+++.   +.  .|+.  
T Consensus         2 ~A~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~e   81 (278)
T PF08631_consen    2 LAWKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSE   81 (278)
T ss_pred             cchhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHH
Confidence            3457789999998888887654  23333222               2         3344444433   21  2332  


Q ss_pred             ---hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           50 ---FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        50 ---~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                         .+...++.++.........++|..+++.+.... +-.+.++-.-+..+.+.++.+++.+++.+|...-         
T Consensus        82 lr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~---------  151 (278)
T PF08631_consen   82 LRLSILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSV---------  151 (278)
T ss_pred             HHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhc---------
Confidence               345566666655444455666777777775542 2235566566777777888888988888886532         


Q ss_pred             HHHHHhcCCCCCCcchHHHHHHHH---HhCCCchHHHHHHHHHHHCCCCCCH
Q 040338          127 RLLIMFQKMPERDLVSWNTMISIL---TRHGFGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus       127 ~a~~~~~~~~~~~~~~~~~li~~~---~~~~~~~~a~~~~~~m~~~g~~p~~  175 (385)
                                .-....+...+..+   ... ....|...++.+....+.|..
T Consensus       152 ----------~~~e~~~~~~l~~i~~l~~~-~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  152 ----------DHSESNFDSILHHIKQLAEK-SPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             ----------ccccchHHHHHHHHHHHHhh-CcHHHHHHHHHHHHHHhCCCh
Confidence                      11234455555544   333 345677777777665555544

It is also involved in sporulation [].

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.30  E-value=4.4  Score=40.46  Aligned_cols=129  Identities=8%  Similarity=-0.011  Sum_probs=87.9

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCCCc---cccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNPSL---FCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      -|..|+..|...|+.++|+++|.+..+...   ......++...+++.+...++....-... -+.-..+++...++|..
T Consensus       506 ~y~~Li~LY~~kg~h~~AL~ll~~l~d~~~~~d~~~~~~~e~ii~YL~~l~~~~~~Li~~y~-~wvl~~~p~~gi~Ift~  584 (877)
T KOG2063|consen  506 KYRELIELYATKGMHEKALQLLRDLVDEDSDTDSFQLDGLEKIIEYLKKLGAENLDLILEYA-DWVLNKNPEAGIQIFTS  584 (877)
T ss_pred             cHHHHHHHHHhccchHHHHHHHHHHhccccccccchhhhHHHHHHHHHHhcccchhHHHHHh-hhhhccCchhheeeeec
Confidence            478999999999999999999999876431   22225566677777777666542211111 12235567777777766


Q ss_pred             H---HHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          166 L---WNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       166 m---~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      -   ....+.|+.      +-.+......+-++..++.+....-.++....+.++..|++.-
T Consensus       585 ~~~~~~~sis~~~------Vl~~l~~~~~~l~I~YLE~li~~~~~~~~~lht~ll~ly~e~v  640 (877)
T KOG2063|consen  585 EDKQEAESISRDD------VLNYLKSKEPKLLIPYLEHLISDNRLTSTLLHTVLLKLYLEKV  640 (877)
T ss_pred             cChhhhccCCHHH------HHHHhhhhCcchhHHHHHHHhHhccccchHHHHHHHHHHHHHH
Confidence            1   112233322      2345667788889999999998888889999999999988754

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.96  E-value=13  Score=36.28  Aligned_cols=146  Identities=15%  Similarity=-0.039  Sum_probs=79.4

Q ss_pred             HHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC-CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCC
Q 040338           94 IDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE-RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFG  172 (385)
Q Consensus        94 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  172 (385)
                      |+.+.+.+.+++|+..-+.....-.                  . .-...+...|..+.-.|++++|-...-.|...   
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~~~~~------------------~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn---  421 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASIGNEE------------------RFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN---  421 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhccCCcc------------------ccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc---
Confidence            6777888888888887655432110                  0 02345777888888888888888877777543   


Q ss_pred             CCHhhHHHHHHHhcCccCccch------------hhHHHHHHHhCCCCchHHHHHHHHHHHh--------cC----CCC-
Q 040338          173 LSSMLYATAFSARASVYDLEWG------------PHLHSRVVHMEPSLDVFVGSGLIDMYLK--------CG----CNG-  227 (385)
Q Consensus       173 p~~~t~~~ll~~~~~~~~~~~a------------~~~~~~~~~~~~~~~~~~~~~li~~~~~--------~g----~~~-  227 (385)
                       +..-|...+..+...++....            -.+++.++-..+.++...|..+++-+-.        ..    ++. 
T Consensus       422 -~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q  500 (846)
T KOG2066|consen  422 -NAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLASDVKGFLELIKEWPGHLYSVLTIISATEPQIKQ  500 (846)
T ss_pred             -hHHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHHHHHHHHHHHHHhCChhhhhhhHHHhhcchHHHh
Confidence             344444444444444433221            1222222222222222222222221100        00    000 


Q ss_pred             CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC
Q 040338          228 IESSIQIGKALVTMYAEGGSTQKADLAFELMSRR  261 (385)
Q Consensus       228 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  261 (385)
                      ...+...-..|...|...+++.+|..++-..+++
T Consensus       501 ~Se~~~L~e~La~LYl~d~~Y~~Al~~ylklk~~  534 (846)
T KOG2066|consen  501 NSESTALLEVLAHLYLYDNKYEKALPIYLKLQDK  534 (846)
T ss_pred             hccchhHHHHHHHHHHHccChHHHHHHHHhccCh
Confidence            2223334445888899999999999999888764

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=91.63  E-value=0.37  Score=27.99  Aligned_cols=30  Identities=20%  Similarity=0.066  Sum_probs=25.9

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCC
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPS  117 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  117 (385)
                      .++..+..+|.+.|++++|.++|++..+.+
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~   31 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALD   31 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            467788899999999999999999987765

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=91.60  E-value=2.5  Score=36.72  Aligned_cols=108  Identities=6%  Similarity=0.025  Sum_probs=67.8

Q ss_pred             hHHHHHHHHHHHHcccchhhHHh-----------------hhhhHHHHHhhhC-------CCChhhHHHHHHHHHhhhcc
Q 040338           10 LPIARKIHAQLISTCLISSIFLQ-----------------LIDDDYRVFCDIG-------PRYLFTYNTMINGGVRCLCV   65 (385)
Q Consensus        10 ~~~a~~~~~~~~~~~~~~~~~~~-----------------~~~~A~~~~~~~~-------~~~~~~~~~li~~~~~~~~~   65 (385)
                      ++....+++.+.+.|+..+.+++                 ....|..+|+.|+       .++-.++..|+..-.. .-.
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~~~~-~~e  156 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAMTSE-DVE  156 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhcccc-cHH
Confidence            45566788888888888877766                 5677888888887       2344556666554110 001


Q ss_pred             CChHHHHHHHHHHHHhccCCCch--HHHhHHHHHHhcCC--hhHHHHHHHhccCCCc
Q 040338           66 GNIKMALHLHGLVKKFYFVSDES--IAKSSIDMHVKCGA--VDYAESAFLRMLNPSL  118 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~--~~~~li~~~~~~g~--~~~a~~~~~~m~~~~~  118 (385)
                      .-.+.+..+++.+.+.|+..+-.  ....++...-....  +..+.++++.+.+.++
T Consensus       157 ~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~  213 (297)
T PF13170_consen  157 ELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGV  213 (297)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCC
Confidence            22466778888888888765443  33334433322222  4477788888888776

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=91.32  E-value=1.4  Score=37.56  Aligned_cols=59  Identities=7%  Similarity=0.072  Sum_probs=36.5

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ++..+++.+...|+.+.+...+++.....+  ...|..++.+|.+.|+...|+..|+.+..
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence            555666666666666666666666665555  56666666666666666666666665543

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=91.26  E-value=0.49  Score=26.07  Aligned_cols=26  Identities=12%  Similarity=0.071  Sum_probs=19.2

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      +|+.|...|.+.|++++|+++|++..
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            46677788888888888888888754

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=90.94  E-value=1.3  Score=39.32  Aligned_cols=108  Identities=12%  Similarity=0.030  Sum_probs=66.1

Q ss_pred             HHHHHcCCChhHHHHHHHhccc------------------CChhhHHHHHHHHHhcCCCCchHHHH------------HH
Q 040338          239 VTMYAEGGSTQKADLAFELMSR------------------RNMISWMVLISAFSQAGVLEKPRFFF------------FF  288 (385)
Q Consensus       239 i~~~~~~g~~~~A~~~~~~m~~------------------~~~~~~~~li~~~~~~g~~~~a~~~~------------~~  288 (385)
                      .+.|.+.|++..|..-|++..+                  .-..++..|..+|.+.+++.+|++..            ..
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KAL  294 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKAL  294 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHH
Confidence            4677788888888888776542                  02245666666777777777776655            44


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHH-HHHHHHhCCCC
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGE-AKKLIDEMPSK  346 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~-A~~~~~~m~~~  346 (385)
                      -.-..+|...|+++.|+..|.++.+..+  ..+-+.++..--+..+..+ ..++|..|..+
T Consensus       295 yRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  295 YRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQKIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4555666677777777777777777666  3333334444333333333 35666666554

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=90.88  E-value=4.8  Score=33.23  Aligned_cols=139  Identities=13%  Similarity=0.056  Sum_probs=88.2

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLR  112 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  112 (385)
                      ++.-|-..++++.+| ..+-.++++    +.+..+..--.++.+-.+..+++-+.....+++.  ...|+...|+..++.
T Consensus       145 RFalaCN~s~KIiEP-IQSRCAiLR----ysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiif--ta~GDMRQalNnLQs  217 (333)
T KOG0991|consen  145 RFALACNQSEKIIEP-IQSRCAILR----YSKLSDQQILKRLLEVAKAEKVNYTDDGLEAIIF--TAQGDMRQALNNLQS  217 (333)
T ss_pred             hhhhhhcchhhhhhh-HHhhhHhhh----hcccCHHHHHHHHHHHHHHhCCCCCcchHHHhhh--hccchHHHHHHHHHH
Confidence            455555555555544 222233333    3335666666677777777777777777666653  357899888888765


Q ss_pred             ccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhc
Q 040338          113 MLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARA  186 (385)
Q Consensus       113 m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  186 (385)
                      -...-.      +-.+..+|+-+..|.+.....++..|. .+++++|.+++.++.+.|..|... .+.+++.+-
T Consensus       218 t~~g~g------~Vn~enVfKv~d~PhP~~v~~ml~~~~-~~~~~~A~~il~~lw~lgysp~Di-i~~~FRv~K  283 (333)
T KOG0991|consen  218 TVNGFG------LVNQENVFKVCDEPHPLLVKKMLQACL-KRNIDEALKILAELWKLGYSPEDI-ITTLFRVVK  283 (333)
T ss_pred             Hhcccc------ccchhhhhhccCCCChHHHHHHHHHHH-hccHHHHHHHHHHHHHcCCCHHHH-HHHHHHHHH
Confidence            433211      112344566666788888888887765 567999999999999999998432 344555443

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=90.81  E-value=1.6  Score=38.23  Aligned_cols=124  Identities=20%  Similarity=0.088  Sum_probs=59.3

Q ss_pred             HHHHHHHcCCChhHHHHHHHhccc-------C--ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHH
Q 040338          237 ALVTMYAEGGSTQKADLAFELMSR-------R--NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHY  307 (385)
Q Consensus       237 ~li~~~~~~g~~~~A~~~~~~m~~-------~--~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~  307 (385)
                      +|.+++.-.+.++++++.|+...+       |  ....|-.|-..|.+..++++|.-+.               .+|..+
T Consensus       127 ~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~---------------~kA~~l  191 (518)
T KOG1941|consen  127 SMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFP---------------CKAAEL  191 (518)
T ss_pred             hHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhh---------------HhHHHH
Confidence            355555556667777777665543       1  2245555555666666665554332               111111


Q ss_pred             HHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCC----CCC----cchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          308 FTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPS----KPT----CVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       308 ~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~p~----~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      .+...-.+.     ....-.|-.+|...|++.+|.+.-++..+    .-|    ......+...|...|+.+.|+.-|+.
T Consensus       192 v~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~  271 (518)
T KOG1941|consen  192 VNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSRGDLERAFRRYEQ  271 (518)
T ss_pred             HHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHHHH
Confidence            111111111     12222344455556665555555544432    122    23334455666666776666666655


Q ss_pred             H
Q 040338          375 L  375 (385)
Q Consensus       375 ~  375 (385)
                      .
T Consensus       272 A  272 (518)
T KOG1941|consen  272 A  272 (518)
T ss_pred             H
Confidence            3

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=90.02  E-value=0.66  Score=24.90  Aligned_cols=31  Identities=13%  Similarity=-0.061  Sum_probs=25.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      +|..+...|...|++++|...|++..+..++
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            5677788888899999999999988887763

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=89.93  E-value=14  Score=33.23  Aligned_cols=50  Identities=14%  Similarity=0.069  Sum_probs=27.9

Q ss_pred             cCChHHHHHHHHHHHHh---ccCCCchHHHhHHHHHHhcCChhHHHHHHHhcc
Q 040338           65 VGNIKMALHLHGLVKKF---YFVSDESIAKSSIDMHVKCGAVDYAESAFLRML  114 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~---g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  114 (385)
                      .|++..|.+.+.+.+..   +..|+.-.|-....+..+.|+.++|+.-.+...
T Consensus       262 ~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al  314 (486)
T KOG0550|consen  262 NGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEAL  314 (486)
T ss_pred             ccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhh
Confidence            56666666666666543   223344445555555555666666666555443

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=89.78  E-value=7.1  Score=29.73  Aligned_cols=84  Identities=17%  Similarity=0.086  Sum_probs=52.9

Q ss_pred             cccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcc-----------------hHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCV-----------------IWGALL  356 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~-----------------~~~~li  356 (385)
                      ...++.+++..+++.|.-.-+  ...-..-.-.+...|++++|.++|++..+.+...                 .|....
T Consensus        21 L~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL~al~Dp~Wr~~A  100 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELLSSAGAPPYGKALLALCLNAKGDAEWHVHA  100 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHHHhcCChHHHHHH
Confidence            347788888888888877666  3333333445678899999999999988763222                 333333


Q ss_pred             HHHHhcCChHHHHHHHHHHHhcc
Q 040338          357 GACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      ......+...++..+.+.+...-
T Consensus       101 ~~~le~~~~~~a~~Lv~al~g~~  123 (153)
T TIGR02561       101 DEVLARDADADAVALVRALLGAQ  123 (153)
T ss_pred             HHHHHhCCCHhHHHHHHHHhccc
Confidence            33444455566666666665433

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=89.76  E-value=1.4  Score=32.49  Aligned_cols=50  Identities=14%  Similarity=0.102  Sum_probs=24.3

Q ss_pred             cccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ...|+++.|++.|......-+  ...||.-..++.-+|+.++|+.=+++..+
T Consensus        54 aE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~Ale  105 (175)
T KOG4555|consen   54 AEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALE  105 (175)
T ss_pred             HhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHH
Confidence            334444444555554444443  44555555555555555555554444443

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.72  E-value=22  Score=35.12  Aligned_cols=92  Identities=14%  Similarity=0.117  Sum_probs=59.6

Q ss_pred             hhhhHHHHHhh-hCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHH
Q 040338           33 LIDDDYRVFCD-IGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFL  111 (385)
Q Consensus        33 ~~~~A~~~~~~-~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~  111 (385)
                      ++++|..-+-+ ++.-++   ..+|.-|..   ..++..-..+++.+.+.|+. +...-+.|+.+|.+.++.++-.++.+
T Consensus       383 df~~A~~qYI~tI~~le~---s~Vi~kfLd---aq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~  455 (933)
T KOG2114|consen  383 DFDEATDQYIETIGFLEP---SEVIKKFLD---AQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFIS  455 (933)
T ss_pred             CHHHHHHHHHHHcccCCh---HHHHHHhcC---HHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHh
Confidence            77777665543 332222   346666555   67888888888899888876 55666788999999988888777766


Q ss_pred             hccCCCccccccchHHHHHHhcC
Q 040338          112 RMLNPSLFCWKFGIIRLLIMFQK  134 (385)
Q Consensus       112 ~m~~~~~~~~~~~~~~a~~~~~~  134 (385)
                      .-. .|.  |--+++.|++++.+
T Consensus       456 ~~~-~g~--~~fd~e~al~Ilr~  475 (933)
T KOG2114|consen  456 KCD-KGE--WFFDVETALEILRK  475 (933)
T ss_pred             cCC-Ccc--eeeeHHHHHHHHHH
Confidence            554 222  33344455544443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=89.68  E-value=5.5  Score=30.13  Aligned_cols=66  Identities=17%  Similarity=0.040  Sum_probs=47.0

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhcc--CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYF--VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL  118 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~  118 (385)
                      ...|+.-...+.    .|++++|.+.|+.+..+-.  +-.....-.|+.+|-+.+++++|...+++..+.++
T Consensus        11 ~~ly~~a~~~l~----~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP   78 (142)
T PF13512_consen   11 QELYQEAQEALQ----KGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHP   78 (142)
T ss_pred             HHHHHHHHHHHH----hCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            345555555543    4999999999999987621  12334556688888999999999999888776554

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=89.61  E-value=5.6  Score=36.68  Aligned_cols=51  Identities=12%  Similarity=0.159  Sum_probs=42.7

Q ss_pred             cCChHHHHHHHHHHHHhccC-CCchHHHhHHHHHHhcCChhHHHHHHHhccC
Q 040338           65 VGNIKMALHLHGLVKKFYFV-SDESIAKSSIDMHVKCGAVDYAESAFLRMLN  115 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  115 (385)
                      .|+.++|.+.+.+|.+.... .+..+...|+.++...+...++..++.+..+
T Consensus       272 lGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdD  323 (539)
T PF04184_consen  272 LGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDD  323 (539)
T ss_pred             hCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcc
Confidence            79999999999999876322 2445788899999999999999999988654

The molecular function of this protein is uncertain.

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.52  E-value=1.1  Score=38.35  Aligned_cols=108  Identities=11%  Similarity=0.039  Sum_probs=73.0

Q ss_pred             hccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHH
Q 040338           81 FYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETL  160 (385)
Q Consensus        81 ~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~  160 (385)
                      .|.+.+..+...++..-....+++++...+-++...--.             ..  .|+... .+.+..+.+ -++++++
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a-------------~~--~~~~~~-~~~irlllk-y~pq~~i  120 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNA-------------WY--LRNWTI-HTWIRLLLK-YDPQKAI  120 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcch-------------hh--hccccH-HHHHHHHHc-cChHHHH
Confidence            455556666677777766677888888777665432110             00  122221 223333333 3577888


Q ss_pred             HHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          161 CTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       161 ~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      .++..=...|+-||.++++.+++.+.+.+++.+|.++.-.|....
T Consensus       121 ~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  121 YTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             HHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            888888888999999999999999999999988888887777664

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=89.51  E-value=12  Score=31.50  Aligned_cols=48  Identities=19%  Similarity=0.234  Sum_probs=31.1

Q ss_pred             HHHHHHHHcCCChhHHHHHHHhcccC--Ch----hhHHHHHHHHHhcCCCCchH
Q 040338          236 KALVTMYAEGGSTQKADLAFELMSRR--NM----ISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       236 ~~li~~~~~~g~~~~A~~~~~~m~~~--~~----~~~~~li~~~~~~g~~~~a~  283 (385)
                      ..+.+-|.+.|.+..|..-+++|.+.  +.    ...-.|.++|...|-.++|.
T Consensus       171 m~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~  224 (254)
T COG4105         171 MAIARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAK  224 (254)
T ss_pred             HHHHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHH
Confidence            35667788888888888888888762  21    33444555666666555553

>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=88.36  E-value=5  Score=31.88  Aligned_cols=64  Identities=6%  Similarity=-0.043  Sum_probs=53.7

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH--hhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS--MLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      ..+..+...|++.|+.++|++.|.++.+....|..  ..+-.+|+...-.+++..+...+.+....
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~  102 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESL  102 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            46788999999999999999999999988666643  45677888889999999998888877664

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.

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.27  E-value=8.3  Score=30.27  Aligned_cols=110  Identities=14%  Similarity=-0.072  Sum_probs=52.2

Q ss_pred             cCCChHHHHHHHHHHHHcccchhhHHh------------hhhhHHHHHhhhCC----CChhhHHHHHHHHHhhhccCChH
Q 040338            6 SLKSLPIARKIHAQLISTCLISSIFLQ------------LIDDDYRVFCDIGP----RYLFTYNTMINGGVRCLCVGNIK   69 (385)
Q Consensus         6 ~~~~~~~a~~~~~~~~~~~~~~~~~~~------------~~~~A~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~~~   69 (385)
                      +.|..++|..-|..+-+.|-.....+.            +.+.|...|+++..    |-..-=.+=+++--.....|.++
T Consensus        70 ~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gsy~  149 (221)
T COG4649          70 QENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGSYD  149 (221)
T ss_pred             HcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhccccHH
Confidence            345555666666666666544443333            56666666665541    11110011111111122355555


Q ss_pred             HHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccC
Q 040338           70 MALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLN  115 (385)
Q Consensus        70 ~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  115 (385)
                      ......+-+...|-+.-...-..|--+-.+.|++.+|.+.|.++..
T Consensus       150 dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         150 DVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            5555555444433333333334444445556666666666666543

>PRK11906 transcriptional regulator; Provisional

Probab=88.04  E-value=15  Score=33.72  Aligned_cols=84  Identities=14%  Similarity=-0.083  Sum_probs=49.6

Q ss_pred             hhhhHHHHHhhhC---CCC---hhh-----HHHHHHHHHhhh-ccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhc
Q 040338           33 LIDDDYRVFCDIG---PRY---LFT-----YNTMINGGVRCL-CVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKC  100 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~---~~~-----~~~li~~~~~~~-~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  100 (385)
                      +.+.|..+|++..   .-|   ...     |+.+...+.... ......+|.++-+...+.+ +.|......+..+..-.
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~  351 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-TVDGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhh
Confidence            6777777777655   333   222     222222211111 1345566777777777665 34667767777777777


Q ss_pred             CChhHHHHHHHhccCCC
Q 040338          101 GAVDYAESAFLRMLNPS  117 (385)
Q Consensus       101 g~~~~a~~~~~~m~~~~  117 (385)
                      ++.+.|...|++....+
T Consensus       352 ~~~~~a~~~f~rA~~L~  368 (458)
T PRK11906        352 GQAKVSHILFEQAKIHS  368 (458)
T ss_pred             cchhhHHHHHHHHhhcC
Confidence            77888888888876554

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=87.57  E-value=1.2  Score=25.15  Aligned_cols=28  Identities=14%  Similarity=0.036  Sum_probs=21.6

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          350 VIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       350 ~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      .+++.|...|...|++++|..++++..+
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            4677888888888888888888888764

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=87.47  E-value=11  Score=28.71  Aligned_cols=102  Identities=10%  Similarity=0.021  Sum_probs=73.6

Q ss_pred             HHHhccCCCc--hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCC-CCCCcchHHHHHHHHHhCC
Q 040338           78 VKKFYFVSDE--SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKM-PERDLVSWNTMISILTRHG  154 (385)
Q Consensus        78 m~~~g~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~li~~~~~~~  154 (385)
                      |.+.+..++.  ...|.++.-.+..+++....++++.+..-..              +.. ...+...|++++.+..+..
T Consensus        28 ~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~--------------~~~~~~~~~ssf~~if~SlsnSs   93 (145)
T PF13762_consen   28 MQEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNT--------------DNIIGWLDNSSFHIIFKSLSNSS   93 (145)
T ss_pred             hhhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhH--------------HHHhhhcccchHHHHHHHHccCh
Confidence            3444444444  3467888888888999999998888743222              001 1356778999999997776


Q ss_pred             C-chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccc
Q 040338          155 F-GFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEW  193 (385)
Q Consensus       155 ~-~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  193 (385)
                      - ---+..+|.-|++.+.+++..-|..++.++.+....+.
T Consensus        94 SaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g~~~~~  133 (145)
T PF13762_consen   94 SAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRGYFHDS  133 (145)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCCcc
Confidence            6 34577899999988899999999999999887644443

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=87.40  E-value=2.8  Score=29.11  Aligned_cols=61  Identities=11%  Similarity=0.069  Sum_probs=45.5

Q ss_pred             chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          156 GFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       156 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      .-++.+-++.+....+.|+.....+.+++|.+.+|+..|.++++-++...- .+...|..++
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~-~~~~~y~~~l   83 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCG-AHKEIYPYIL   83 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc-CchhhHHHHH
Confidence            335667777777788999999999999999999999999999998874421 1333554443

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.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=87.16  E-value=18  Score=31.06  Aligned_cols=129  Identities=12%  Similarity=0.004  Sum_probs=79.6

Q ss_pred             HHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH-------------HHHHHHHHhcccCChhhH
Q 040338          241 MYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKG  304 (385)
Q Consensus       241 ~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~-------------~~~~l~~~~~~~~~~~~a  304 (385)
                      .....|++.+|...|+....   .+...--.++.+|...|+.+.|..++             ....-|+...+.....+.
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~~  222 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPEI  222 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCCH
Confidence            44566778888887776654   24455556777788888888777777             211223344444444444


Q ss_pred             HHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CCcchHHHHHHHHHhcCChHHHH
Q 040338          305 KHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PTCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       305 ~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      ..+-........ ...-..+...+...|+.++|.+.+=.+..+    -|...-..|+..+.--|..+.+.
T Consensus       223 ~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~~  292 (304)
T COG3118         223 QDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPADPLV  292 (304)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCCHHH
Confidence            444444444443 455556777888889999888877666553    45555667777777766444433

>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=86.64  E-value=14  Score=29.01  Aligned_cols=46  Identities=11%  Similarity=0.035  Sum_probs=25.1

Q ss_pred             HHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCch
Q 040338          161 CTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDV  210 (385)
Q Consensus       161 ~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  210 (385)
                      ++++.+.+.|++|+...|..+++.+.+.|.+.    .+..+++.++-+|.
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~----~L~qllq~~Vi~DS   60 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFS----QLHQLLQYHVIPDS   60 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHH----HHHHHHhhcccCCc
Confidence            44455555666666666666666666666532    33444444444433

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=86.27  E-value=0.73  Score=25.04  Aligned_cols=22  Identities=9%  Similarity=-0.013  Sum_probs=12.1

Q ss_pred             CcchHHHHHHHHHhcCChHHHH
Q 040338          348 TCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       348 ~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      +...|..+...|...|++++|+
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            3445555555555555555553

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.23  E-value=12  Score=35.38  Aligned_cols=132  Identities=11%  Similarity=-0.080  Sum_probs=70.7

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCC-CccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNP-SLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      .-+.++..+.+.|..++|+++--.-.++ .+....|+++.|.++..+  ..+..-|..|-.+....+++..|.+.|....
T Consensus       616 ~rt~va~Fle~~g~~e~AL~~s~D~d~rFelal~lgrl~iA~~la~e--~~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~  693 (794)
T KOG0276|consen  616 IRTKVAHFLESQGMKEQALELSTDPDQRFELALKLGRLDIAFDLAVE--ANSEVKWRQLGDAALSAGELPLASECFLRAR  693 (794)
T ss_pred             hhhhHHhHhhhccchHhhhhcCCChhhhhhhhhhcCcHHHHHHHHHh--hcchHHHHHHHHHHhhcccchhHHHHHHhhc
Confidence            3445556666666666666553111000 001111333333333332  2455667777777777777777777776654


Q ss_pred             HCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC
Q 040338          168 NHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS  247 (385)
Q Consensus       168 ~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~  247 (385)
                      .         |..|+-.+...|+.+....+-....+.|..                            |.-..+|...|+
T Consensus       694 d---------~~~LlLl~t~~g~~~~l~~la~~~~~~g~~----------------------------N~AF~~~~l~g~  736 (794)
T KOG0276|consen  694 D---------LGSLLLLYTSSGNAEGLAVLASLAKKQGKN----------------------------NLAFLAYFLSGD  736 (794)
T ss_pred             c---------hhhhhhhhhhcCChhHHHHHHHHHHhhccc----------------------------chHHHHHHHcCC
Confidence            3         334454555556655444444444444431                            333456667788


Q ss_pred             hhHHHHHHHhcc
Q 040338          248 TQKADLAFELMS  259 (385)
Q Consensus       248 ~~~A~~~~~~m~  259 (385)
                      ++++.+++.+-.
T Consensus       737 ~~~C~~lLi~t~  748 (794)
T KOG0276|consen  737 YEECLELLISTQ  748 (794)
T ss_pred             HHHHHHHHHhcC
Confidence            888888876553

>PRK11906 transcriptional regulator; Provisional

Probab=86.21  E-value=28  Score=32.14  Aligned_cols=138  Identities=14%  Similarity=-0.007  Sum_probs=82.9

Q ss_pred             CChHHHHHHHHHHHHh-ccCCC-chHHHhHHHHHHhc---------CChhHHHHHHHhccCCCccccccchHHHHHHhcC
Q 040338           66 GNIKMALHLHGLVKKF-YFVSD-ESIAKSSIDMHVKC---------GAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQK  134 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~-g~~~~-~~~~~~li~~~~~~---------g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~  134 (385)
                      ...+.|+.+|.+.... ...|+ ...|..+..++...         ....+|.+.-++..+.+                 
T Consensus       272 ~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-----------------  334 (458)
T PRK11906        272 ESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-----------------  334 (458)
T ss_pred             HHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-----------------
Confidence            3456677777777622 23333 34455444443322         23455666666666655                 


Q ss_pred             CCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCch-HH
Q 040338          135 MPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDV-FV  212 (385)
Q Consensus       135 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~  212 (385)
                        +.|..+...+..+..-.++++.|..+|++...  +.|| ..+|...-..+.-.|+.++|.+.+++..+..+.--. .+
T Consensus       335 --~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~--L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~  410 (458)
T PRK11906        335 --TVDGKILAIMGLITGLSGQAKVSHILFEQAKI--HSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVV  410 (458)
T ss_pred             --CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhh--cCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHH
Confidence              46666666666666777889999999988876  4564 334444444455568888998888887766543322 23


Q ss_pred             HHHHHHHHHhcC
Q 040338          213 GSGLIDMYLKCG  224 (385)
Q Consensus       213 ~~~li~~~~~~g  224 (385)
                      .--.++.|+..+
T Consensus       411 ~~~~~~~~~~~~  422 (458)
T PRK11906        411 IKECVDMYVPNP  422 (458)
T ss_pred             HHHHHHHHcCCc
Confidence            333344666665

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=86.19  E-value=21  Score=30.72  Aligned_cols=144  Identities=11%  Similarity=-0.002  Sum_probs=81.0

Q ss_pred             HHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH
Q 040338           96 MHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus        96 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  175 (385)
                      .....|+..+|..+|+......                   +.+...--.+..+|...|+.+.|..++..+...--....
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~-------------------~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~  203 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAA-------------------PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAA  203 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhC-------------------cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHH
Confidence            3445666777776666654433                   233444555677777778888877777776433212222


Q ss_pred             hhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHH
Q 040338          176 MLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAF  255 (385)
Q Consensus       176 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~  255 (385)
                      +....-|..+.+.....+...+-+..-..                        +-|...--.+...+...|+.+.|.+.+
T Consensus       204 ~~l~a~i~ll~qaa~~~~~~~l~~~~aad------------------------Pdd~~aa~~lA~~~~~~g~~e~Ale~L  259 (304)
T COG3118         204 HGLQAQIELLEQAAATPEIQDLQRRLAAD------------------------PDDVEAALALADQLHLVGRNEAALEHL  259 (304)
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHhC------------------------CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            22223344444444444444444443322                        123444456667777778888888877


Q ss_pred             HhcccC-----ChhhHHHHHHHHHhcCCCCch
Q 040338          256 ELMSRR-----NMISWMVLISAFSQAGVLEKP  282 (385)
Q Consensus       256 ~~m~~~-----~~~~~~~li~~~~~~g~~~~a  282 (385)
                      -.+.++     |...-..|++.+.-.|..+.+
T Consensus       260 l~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~  291 (304)
T COG3118         260 LALLRRDRGFEDGEARKTLLELFEAFGPADPL  291 (304)
T ss_pred             HHHHHhcccccCcHHHHHHHHHHHhcCCCCHH
Confidence            666543     556666777777666655543

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=86.09  E-value=6.6  Score=27.53  Aligned_cols=88  Identities=14%  Similarity=0.067  Sum_probs=46.2

Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHH
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNT  145 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  145 (385)
                      +..++|.-+-+.+...+-. ...+--+-+..+...|++++|..+.+.                      ++.||...|-+
T Consensus        19 HcHqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~----------------------~~~pdlepw~A   75 (115)
T TIGR02508        19 HCHQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNK----------------------LCYPDLEPWLA   75 (115)
T ss_pred             hHHHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCC----------------------CCCchHHHHHH
Confidence            4455666555555543211 111211222344455666666665533                      33678777766


Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHH
Q 040338          146 MISILTRHGFGFETLCTFIELWNHGFGLSSMLYA  179 (385)
Q Consensus       146 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~  179 (385)
                      |-..  +.|..++...-+.+|...| .|...+|.
T Consensus        76 Lce~--rlGl~s~l~~rl~rla~sg-~p~lq~Fa  106 (115)
T TIGR02508        76 LCEW--RLGLGSALESRLNRLAASG-DPRLQTFV  106 (115)
T ss_pred             HHHH--hhccHHHHHHHHHHHHhCC-CHHHHHHH
Confidence            6543  5666666666666676654 34444443

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=86.04  E-value=6.3  Score=31.75  Aligned_cols=78  Identities=9%  Similarity=-0.067  Sum_probs=53.5

Q ss_pred             ChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHH
Q 040338           67 NIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTM  146 (385)
Q Consensus        67 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l  146 (385)
                      .=+.|.+.|-.+...+.--++.....|...|. ..+.++++.++.+..+               +...-..+|+..+.+|
T Consensus       121 ~d~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~---------------l~~~~~~~n~eil~sL  184 (203)
T PF11207_consen  121 GDQEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALE---------------LSNPDDNFNPEILKSL  184 (203)
T ss_pred             CcHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHH---------------hcCCCCCCCHHHHHHH
Confidence            33677777777777765556666666666665 5778888888765432               2222225778888888


Q ss_pred             HHHHHhCCCchHHH
Q 040338          147 ISILTRHGFGFETL  160 (385)
Q Consensus       147 i~~~~~~~~~~~a~  160 (385)
                      .+.+.+.|+++.|.
T Consensus       185 as~~~~~~~~e~AY  198 (203)
T PF11207_consen  185 ASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHhcchhhhh
Confidence            88888888888774

>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=86.01  E-value=14  Score=28.60  Aligned_cols=64  Identities=14%  Similarity=-0.005  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhH-HHHHHhcCChhHHHHHHHhccCC
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSS-IDMHVKCGAVDYAESAFLRMLNP  116 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l-i~~~~~~g~~~~a~~~~~~m~~~  116 (385)
                      ..+.||..+......++.+.+..+++.+.-.  .|.......+ ...+.+.|++.+|.++|+++...
T Consensus         9 iv~gLie~~~~al~~~~~~D~e~lL~ALrvL--RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen    9 IVGGLIEVLSVALRLGDPDDAEALLDALRVL--RPEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HHHHHHHHHHHHHccCChHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            4566777766666678999999999988764  5554433332 35566789999999999887553

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=85.87  E-value=1  Score=24.41  Aligned_cols=31  Identities=6%  Similarity=0.022  Sum_probs=23.4

Q ss_pred             HHHHHhccCCCchHHHhHHHHHHhcCChhHHH
Q 040338           76 GLVKKFYFVSDESIAKSSIDMHVKCGAVDYAE  107 (385)
Q Consensus        76 ~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~  107 (385)
                      ++.++.. |-+...|+.+...|...|++++|+
T Consensus         3 ~kAie~~-P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELN-PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHC-CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            4444443 447788999999999999998885

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=85.69  E-value=18  Score=29.60  Aligned_cols=66  Identities=8%  Similarity=-0.158  Sum_probs=44.5

Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      -+.+||.|--.+...|+++.|.+.|+...+.+..-+-...|--|. +.=.|++.-|.+-+-..-+..
T Consensus        98 m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi~-~YY~gR~~LAq~d~~~fYQ~D  163 (297)
T COG4785          98 MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIA-LYYGGRYKLAQDDLLAFYQDD  163 (297)
T ss_pred             cHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhcccee-eeecCchHhhHHHHHHHHhcC
Confidence            356899999899999999999999999987543333333333333 233567777766555555443

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.48  E-value=20  Score=29.93  Aligned_cols=52  Identities=10%  Similarity=0.163  Sum_probs=35.3

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHH
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLI  340 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~  340 (385)
                      |...|-.+....++..|...++.-.+.+.      ..+...|+.+|- .|+.+++.+++
T Consensus       193 ~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd-~gD~E~~~kvl  250 (308)
T KOG1585|consen  193 YVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYD-EGDIEEIKKVL  250 (308)
T ss_pred             HHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhc-cCCHHHHHHHH
Confidence            44555566667788888888887555444      566666777664 67778777765

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=85.38  E-value=23  Score=30.43  Aligned_cols=137  Identities=8%  Similarity=-0.025  Sum_probs=80.2

Q ss_pred             ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCC-----CCCcchHHHHHHHHHhC-C-
Q 040338           82 YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMP-----ERDLVSWNTMISILTRH-G-  154 (385)
Q Consensus        82 g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~-----~~~~~~~~~li~~~~~~-~-  154 (385)
                      |.+++..-.-.+++.....-...+... |..+.+     .|..+.+|+++|+...     -.|..+-..|++..... + 
T Consensus       107 g~~Lt~~Dli~FL~~~i~~~~~~k~~~-Y~~LVk-----~N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~  180 (292)
T PF13929_consen  107 GCELTKEDLISFLKLVIINLSSNKSFN-YWDLVK-----RNKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENT  180 (292)
T ss_pred             CCCCcHHHHHHHHHHHHhccccccchH-HHHHHH-----hhHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhcccc
Confidence            555555555555555444333333222 222222     2245677777777432     24666677777777662 2 


Q ss_pred             CchHHHHHHHHHHH-CCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh-CCCCchHHHHHHHHHHHhcC
Q 040338          155 FGFETLCTFIELWN-HGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM-EPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       155 ~~~~a~~~~~~m~~-~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~li~~~~~~g  224 (385)
                      ....-.++.+-+.. .|-.++..+...++..+++.+++..-.++++..... ++..|...|..+|+...+.|
T Consensus       181 ~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sg  252 (292)
T PF13929_consen  181 KLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESG  252 (292)
T ss_pred             chhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcC
Confidence            22223344444433 346788888889999999999999999988887665 55556666655555554444

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.29  E-value=25  Score=30.86  Aligned_cols=140  Identities=9%  Similarity=-0.042  Sum_probs=98.7

Q ss_pred             hCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCch
Q 040338          152 RHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESS  231 (385)
Q Consensus       152 ~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~  231 (385)
                      ..|+..+|-..++++.+. .+.|...+...=.+|.-.|+...-...++.+... ..+|...|+-+-.             
T Consensus       115 ~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~G-------------  179 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHG-------------  179 (491)
T ss_pred             ccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHH-------------
Confidence            367777887788888765 5557777777778888888888888888877654 2345444432222             


Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH----------------HHHHHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF----------------FFVSLL  292 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~----------------~~~~l~  292 (385)
                           ...-++..+|-+++|++.-++-.+   -|..+..++...+-..|+..++.++.                -|-...
T Consensus       180 -----myaFgL~E~g~y~dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~A  254 (491)
T KOG2610|consen  180 -----MYAFGLEECGIYDDAEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTA  254 (491)
T ss_pred             -----HHHhhHHHhccchhHHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHH
Confidence                 223455678899999988887765   36667777888888889999998887                333344


Q ss_pred             HHhcccCChhhHHHHHHHH
Q 040338          293 SGCSHSGPVTKGKHYFTAM  311 (385)
Q Consensus       293 ~~~~~~~~~~~a~~~~~~~  311 (385)
                      -.+...+.++.|..+|+.-
T Consensus       255 l~~iE~aeye~aleIyD~e  273 (491)
T KOG2610|consen  255 LFHIEGAEYEKALEIYDRE  273 (491)
T ss_pred             HhhhcccchhHHHHHHHHH
Confidence            4556678899999888863

>PF13934 ELYS: Nuclear pore complex assembly

Probab=85.08  E-value=21  Score=29.71  Aligned_cols=72  Identities=17%  Similarity=0.175  Sum_probs=43.1

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhc
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSH  362 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~  362 (385)
                      .++.+....|+.+.|.+++....-... ......++.. ..++.+.||..+-+...++-....+..++..+...
T Consensus       113 ~Il~~L~~~~~~~lAL~y~~~~~p~l~s~~~~~~~~~~-La~~~v~EAf~~~R~~~~~~~~~l~e~l~~~~~~~  185 (226)
T PF13934_consen  113 KILQALLRRGDPKLALRYLRAVGPPLSSPEALTLYFVA-LANGLVTEAFSFQRSYPDELRRRLFEQLLEHCLEE  185 (226)
T ss_pred             HHHHHHHHCCChhHHHHHHHhcCCCCCCHHHHHHHHHH-HHcCCHHHHHHHHHhCchhhhHHHHHHHHHHHHHH
Confidence            455555556667777777766544333 3333434444 55688888888877776543345666777766643

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=84.92  E-value=1.6  Score=22.98  Aligned_cols=28  Identities=11%  Similarity=-0.067  Sum_probs=19.9

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          354 ALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       354 ~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      .+..++.+.|++++|.+.|+++++..|.
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~~~P~   32 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIKRYPD   32 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence            3556677777888888888887776654

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=84.83  E-value=1.8  Score=23.16  Aligned_cols=28  Identities=11%  Similarity=-0.018  Sum_probs=21.0

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      .+|..+...|...|++++|+..|++..+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            3567777888888888888888888766

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=84.02  E-value=6.4  Score=31.65  Aligned_cols=60  Identities=3%  Similarity=-0.114  Sum_probs=31.7

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  346 (385)
                      .|..-..+..+.+.++.|+.--.+....++  .....--..+|.+..++++|+.=|..+.+.
T Consensus       136 ly~Nraaa~iKl~k~e~aI~dcsKaiel~pty~kAl~RRAeayek~ek~eealeDyKki~E~  197 (271)
T KOG4234|consen  136 LYSNRAAALIKLRKWESAIEDCSKAIELNPTYEKALERRAEAYEKMEKYEEALEDYKKILES  197 (271)
T ss_pred             HHhhhHHHHHHhhhHHHHHHHHHhhHhcCchhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh
Confidence            455555555555666666555555555544  222223344555556666666666655553

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=83.80  E-value=2.4  Score=23.76  Aligned_cols=28  Identities=18%  Similarity=0.092  Sum_probs=22.6

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      .+++.|...|...|++++|..++++...
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            4678888899999999999999888754

>PRK13342 recombination factor protein RarA; Reviewed

Probab=83.27  E-value=38  Score=31.25  Aligned_cols=138  Identities=10%  Similarity=-0.122  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHHHHh---cc-CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           68 IKMALHLHGLVKKF---YF-VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        68 ~~~a~~~~~~m~~~---g~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      .++...++......   |+ ..+......++...  .|+...++.+++.....+.......+.++..........+...+
T Consensus       153 ~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s--~Gd~R~aln~Le~~~~~~~~It~~~v~~~~~~~~~~~d~~~~~~  230 (413)
T PRK13342        153 EEDIEQLLKRALEDKERGLVELDDEALDALARLA--NGDARRALNLLELAALGVDSITLELLEEALQKRAARYDKDGDEH  230 (413)
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhC--CCCHHHHHHHHHHHHHccCCCCHHHHHHHHhhhhhccCCCccHH
Confidence            45666666665432   43 45555555555433  68899998888876432111111222222221111112222344


Q ss_pred             HHHHHHHHh---CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccC-----ccchhhHHHHHHHhCCC
Q 040338          144 NTMISILTR---HGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYD-----LEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       144 ~~li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~-----~~~a~~~~~~~~~~~~~  207 (385)
                      ..+++++.+   ..+++.|+.++..|.+.|..|....-..++.++-..|.     ..-|...++.....|.+
T Consensus       231 ~~~isa~~ks~rgsd~~aal~~l~~~l~~G~d~~~i~rrl~~~a~edig~a~~~~~~~~~~~~~~~~~~g~p  302 (413)
T PRK13342        231 YDLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASEDIGLADPNALQVAVAAADAVERIGMP  302 (413)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHHhCCc
Confidence            555666555   47899999999999999988876666666666555443     22344445555555653

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.23  E-value=49  Score=32.49  Aligned_cols=86  Identities=9%  Similarity=0.014  Sum_probs=66.1

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTK  366 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~  366 (385)
                      +.+--+.-+...|+-.+|.++-.+.+-.. ...|--=+.+++..+++++-+++-+.++   .+.-|.-++.+|.+.|+.+
T Consensus       686 Sl~dTv~~li~~g~~k~a~ql~~~Fkipd-Kr~~wLk~~aLa~~~kweeLekfAkskk---sPIGy~PFVe~c~~~~n~~  761 (829)
T KOG2280|consen  686 SLHDTVTTLILIGQNKRAEQLKSDFKIPD-KRLWWLKLTALADIKKWEELEKFAKSKK---SPIGYLPFVEACLKQGNKD  761 (829)
T ss_pred             cHHHHHHHHHHccchHHHHHHHHhcCCcc-hhhHHHHHHHHHhhhhHHHHHHHHhccC---CCCCchhHHHHHHhcccHH
Confidence            66666777777888888888877654333 3445556788999999999888877665   3678889999999999999


Q ss_pred             HHHHHHHHHH
Q 040338          367 LAELVMRNLL  376 (385)
Q Consensus       367 ~a~~~~~~~~  376 (385)
                      +|.+.+-+.-
T Consensus       762 EA~KYiprv~  771 (829)
T KOG2280|consen  762 EAKKYIPRVG  771 (829)
T ss_pred             HHhhhhhccC
Confidence            9998876653

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=83.16  E-value=4.2  Score=28.62  Aligned_cols=47  Identities=13%  Similarity=0.091  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          158 ETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       158 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      +..+-+..+....+.|+.....+.+++|.+.+|+..|.++++-++..
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            56666777777788999999999999999999999999999988775

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 ....

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=82.88  E-value=2.5  Score=21.16  Aligned_cols=19  Identities=26%  Similarity=0.296  Sum_probs=9.2

Q ss_pred             HHHHHHccCCHHHHHHHHH
Q 040338          323 MVDLLGLSGLLGEAKKLID  341 (385)
Q Consensus       323 li~~~~~~g~~~~A~~~~~  341 (385)
                      +...+...|++++|..+++
T Consensus         7 la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    7 LARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHcCCHHHHHHHHh
Confidence            4444445555555554443

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>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=82.75  E-value=5.8  Score=31.54  Aligned_cols=89  Identities=10%  Similarity=0.035  Sum_probs=58.2

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---CCcchHHH---H
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---PTCVIWGA---L  355 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p~~~~~~~---l  355 (385)
                      .+..+..-|.+.|+.+.|.+.+.++.....     ...+-.+|....-.+++..+...+.+...-   +.......   .
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~  117 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKV  117 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            677788888888888888888888777654     566667777777888888888887776653   21111111   1


Q ss_pred             HH--HHHhcCChHHHHHHHHHH
Q 040338          356 LG--ACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       356 i~--~~~~~g~~~~a~~~~~~~  375 (385)
                      ..  ++...+++.+|-+.|-+.
T Consensus       118 ~~gL~~l~~r~f~~AA~~fl~~  139 (177)
T PF10602_consen  118 YEGLANLAQRDFKEAAELFLDS  139 (177)
T ss_pred             HHHHHHHHhchHHHHHHHHHcc
Confidence            12  234566777776666544

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.

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.56  E-value=22  Score=28.03  Aligned_cols=140  Identities=11%  Similarity=-0.005  Sum_probs=92.7

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHH-hHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAK-SSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~-~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ..|..-+.    ..+.+..++|+.-|.++.+.|...-+..-. ......++.|+...|...|+++-....          
T Consensus        60 d~flaAL~----lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~----------  125 (221)
T COG4649          60 DAFLAALK----LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTS----------  125 (221)
T ss_pred             HHHHHHHH----HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCC----------
Confidence            34555554    344799999999999999988764433322 233456778999999999998865443          


Q ss_pred             HHHhcCCCCCCcc-hHHHH--HHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          129 LIMFQKMPERDLV-SWNTM--ISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       129 ~~~~~~~~~~~~~-~~~~l--i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                              .|-+. -...|  ...+..+|.++++..-.+-+-..|-+.-...-..|--+-.+.|++.+|.+.|..+....
T Consensus       126 --------~P~~~rd~ARlraa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da  197 (221)
T COG4649         126 --------IPQIGRDLARLRAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDA  197 (221)
T ss_pred             --------CcchhhHHHHHHHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccc
Confidence                    23222 11111  23456788899888888777655443334444566667778999999999999988765


Q ss_pred             CCCchH
Q 040338          206 PSLDVF  211 (385)
Q Consensus       206 ~~~~~~  211 (385)
                      ..|...
T Consensus       198 ~aprni  203 (221)
T COG4649         198 QAPRNI  203 (221)
T ss_pred             cCcHHH
Confidence            555443

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.44  E-value=20  Score=31.41  Aligned_cols=136  Identities=15%  Similarity=-0.007  Sum_probs=84.6

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCC---Cccccc-------------cchHHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNP---SLFCWK-------------FGIIRL  128 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~~~~-------------~~~~~a  128 (385)
                      +|+..+|-..++++.+. +|.|...++-.=++|.-.|+...-...++++...   +.+++.             |.+++|
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            57777777777777765 4556677777777777777777777777766433   332222             666666


Q ss_pred             HHHhcCCC---CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC---CCCCCHhhHHHHHHHhcCccCccchhhHHHHH
Q 040338          129 LIMFQKMP---ERDLVSWNTMISILTRHGFGFETLCTFIELWNH---GFGLSSMLYATAFSARASVYDLEWGPHLHSRV  201 (385)
Q Consensus       129 ~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  201 (385)
                      ++.-++-.   +.|.-.-.++...+--.|+.+++.+++.+-...   +--.-.+-|-...-.+...+.++.|+++|+.=
T Consensus       195 Ek~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~e  273 (491)
T KOG2610|consen  195 EKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDRE  273 (491)
T ss_pred             HHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHHH
Confidence            66555543   344555566777777788888888877654321   11111222333344566778899999988753

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=82.30  E-value=1.9  Score=25.07  Aligned_cols=24  Identities=13%  Similarity=0.066  Sum_probs=15.3

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhc
Q 040338          355 LLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       355 li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                      |..+|...|+.+.|.++++++...
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~   28 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEE   28 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHc
Confidence            556666666666666666666643

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>smart00028 TPR Tetratricopeptide repeats

Probab=82.16  E-value=2.9  Score=21.10  Aligned_cols=30  Identities=20%  Similarity=-0.054  Sum_probs=21.4

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      .|..+...+...|+++.|...+++.++..+
T Consensus         3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~   32 (34)
T smart00028        3 ALYNLGNAYLKLGDYDEALEYYEKALELDP   32 (34)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHccCC
Confidence            456667777777788888887777776554

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=81.65  E-value=10  Score=31.01  Aligned_cols=76  Identities=11%  Similarity=0.020  Sum_probs=52.3

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      .+.-+..+.+.+.+.+++....+-.+..                   +.|..+-..++..+|-.|+|++|...++..-..
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkak-------------------Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l   64 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAK-------------------PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATL   64 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcC-------------------CccccchhHHHHHHhhcchHHHHHHHHHHHhhc
Confidence            3445566777778888887776554443                   346667778889999999999998888776543


Q ss_pred             C--CCCCHhhHHHHHHH
Q 040338          170 G--FGLSSMLYATAFSA  184 (385)
Q Consensus       170 g--~~p~~~t~~~ll~~  184 (385)
                      .  ..+-..+|..+|++
T Consensus        65 ~p~~t~~a~lyr~lir~   81 (273)
T COG4455          65 SPQDTVGASLYRHLIRC   81 (273)
T ss_pred             CcccchHHHHHHHHHHH
Confidence            2  33445677777764

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=81.04  E-value=12  Score=32.05  Aligned_cols=58  Identities=10%  Similarity=-0.112  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHH
Q 040338          319 YFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLL  376 (385)
Q Consensus       319 ~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  376 (385)
                      ++......|..+|.+.+|.++.+....-  .+...|..|++.++..||--.+.+-++.+.
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~la~~gD~is~~khyerya  340 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERYA  340 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcChhhhHHHHHHHHHHHHhccchhhhhHHHHHH
Confidence            3444566788899999999999888763  466678889999999998766666666553

>PRK09687 putative lyase; Provisional

Probab=80.58  E-value=37  Score=29.34  Aligned_cols=213  Identities=12%  Similarity=-0.046  Sum_probs=100.8

Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCcc----chhhHHHHHHHhCCCCchHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLE----WGPHLHSRVVHMEPSLDVFV  212 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~----~a~~~~~~~~~~~~~~~~~~  212 (385)
                      .+|..+.-..+.++...|. +++...+..+...   +|...-...+.+++..|+..    ++...+..+..  -.++..+
T Consensus        34 d~d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~--~D~d~~V  107 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLAL--EDKSACV  107 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHh--cCCCHHH
Confidence            5666666677777776664 3444444445432   34444445556666666532    34444444422  2355556


Q ss_pred             HHHHHHHHHhcCCCCCCc---------------hhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcC
Q 040338          213 GSGLIDMYLKCGCNGIES---------------SIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAG  277 (385)
Q Consensus       213 ~~~li~~~~~~g~~~~~~---------------~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g  277 (385)
                      -...+.+++..+.....|               +..+-...+.++++.++.+....+..-+.++|...-..-+.++.+.+
T Consensus       108 R~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~D~~~~VR~~a~~aLg~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~~~  187 (280)
T PRK09687        108 RASAINATGHRCKKNPLYSPKIVEQSQITAFDKSTNVRFAVAFALSVINDEAAIPLLINLLKDPNGDVRNWAAFALNSNK  187 (280)
T ss_pred             HHHHHHHHhcccccccccchHHHHHHHHHhhCCCHHHHHHHHHHHhccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhcCC
Confidence            656666666554333222               22233333444444444222222222222333333333333333221


Q ss_pred             CCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHH
Q 040338          278 VLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLG  357 (385)
Q Consensus       278 ~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~  357 (385)
                      .                     ....+...+..+.......+-...+.++.+.|+ ..|...+-+..+.++  .....+.
T Consensus       188 ~---------------------~~~~~~~~L~~~L~D~~~~VR~~A~~aLg~~~~-~~av~~Li~~L~~~~--~~~~a~~  243 (280)
T PRK09687        188 Y---------------------DNPDIREAFVAMLQDKNEEIRIEAIIGLALRKD-KRVLSVLIKELKKGT--VGDLIIE  243 (280)
T ss_pred             C---------------------CCHHHHHHHHHHhcCCChHHHHHHHHHHHccCC-hhHHHHHHHHHcCCc--hHHHHHH
Confidence            1                     122334444444443334555556666666666 344444444444333  2335666


Q ss_pred             HHHhcCChHHHHHHHHHHHhccc
Q 040338          358 ACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       358 ~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      ++...|+. +|...+..+.+..+
T Consensus       244 ALg~ig~~-~a~p~L~~l~~~~~  265 (280)
T PRK09687        244 AAGELGDK-TLLPVLDTLLYKFD  265 (280)
T ss_pred             HHHhcCCH-hHHHHHHHHHhhCC
Confidence            66666663 56666666665443

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=80.26  E-value=45  Score=30.10  Aligned_cols=145  Identities=14%  Similarity=0.049  Sum_probs=89.6

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh--cCChhHHHHHH
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK--CGAVDYAESAF  110 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~--~g~~~~a~~~~  110 (385)
                      ++..+.+.|..-+  .-..|.+|=.|+.. ...|+-..|.++-.+..+. +..|....-.|+.+-..  .|+.++|.+-|
T Consensus        68 sP~t~~Ryfr~rK--RdrgyqALStGliA-agAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kf  143 (531)
T COG3898          68 SPYTARRYFRERK--RDRGYQALSTGLIA-AGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKF  143 (531)
T ss_pred             CcHHHHHHHHHHH--hhhHHHHHhhhhhh-hccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHH
Confidence            6667777776533  22356666666665 3368888988887666543 45566666666654443  69999999999


Q ss_pred             HhccCCCccccccchHHHHHHhcCCCCCCcch--HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-HhhHHHHHHHhcC
Q 040338          111 LRMLNPSLFCWKFGIIRLLIMFQKMPERDLVS--WNTMISILTRHGFGFETLCTFIELWNHGFGLS-SMLYATAFSARAS  187 (385)
Q Consensus       111 ~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~  187 (385)
                      +-|...                     |....  .-.|.-.--+.|..+.|..+-+..-+  ..|. .......+...+.
T Consensus       144 eAMl~d---------------------PEtRllGLRgLyleAqr~GareaAr~yAe~Aa~--~Ap~l~WA~~AtLe~r~~  200 (531)
T COG3898         144 EAMLDD---------------------PETRLLGLRGLYLEAQRLGAREAARHYAERAAE--KAPQLPWAARATLEARCA  200 (531)
T ss_pred             HHHhcC---------------------hHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHh--hccCCchHHHHHHHHHHh
Confidence            999642                     11111  11122222456667666666666544  2343 3455667777778


Q ss_pred             ccCccchhhHHHHHHHh
Q 040338          188 VYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       188 ~~~~~~a~~~~~~~~~~  204 (385)
                      .||++.|+++.+.-+..
T Consensus       201 ~gdWd~AlkLvd~~~~~  217 (531)
T COG3898         201 AGDWDGALKLVDAQRAA  217 (531)
T ss_pred             cCChHHHHHHHHHHHHH
Confidence            88888888887766554

---

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	385
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.1 bits (98), Expect = 3e-04
 Identities = 39/263 (14%), Positives = 75/263 (28%), Gaps = 73/263 (27%)

Query: 7   LKSLPIARKIHAQLISTCLISSIFLQLIDDD------YRVFCDIGPRYLFT------YNT 54
           L+ L +  K +      CL       L+  +      +  F ++  + L T       + 
Sbjct: 234 LRRL-LKSKPYEN----CL-------LVLLNVQNAKAWNAF-NLSCKILLTTRFKQVTDF 280

Query: 55  MINGGVRCLCVGNIKMALHLH---GLVKKFYFVSDES---------------IAKSSIDM 96
           +       + + +  M L       L+ K+     +                IA+S  D 
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340

Query: 97  --------HVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQ---KMPERDLVS-WN 144
                   HV C  +     + L +L P+ +   F     L +F     +P   L   W 
Sbjct: 341 LATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF---DRLSVFPPSAHIPTILLSLIWF 397

Query: 145 TMISILTRHGFGFETLC---TFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRV 201
            +I                 + +E       +S  + +     +  + +      LH  +
Sbjct: 398 DVIKSDVMV---VVNKLHKYSLVEKQPKESTIS--IPSIYLELKVKLENE---YALHRSI 449

Query: 202 VHMEPSLDVFVGSGL----IDMY 220
           V        F    L    +D Y
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQY 472

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	385
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.95
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.92
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.89
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.88
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.88
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.84
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.84
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.82
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.82
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.81
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.79
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.78
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.78
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.77
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.75
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.75
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.73
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.72
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.71
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.69
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.69
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.69
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.66
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.61
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.58
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.58
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.58
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.58
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.57
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.55
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.54
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.53
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.52
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.5
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.49
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.48
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.47
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.46
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.46
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.46
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.46
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.45
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.44
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.43
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.43
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.43
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.42
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.42
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.41
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.41
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.41
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.41
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.4
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.4
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.39
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.39
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.38
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.38
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.33
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.33
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.32
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.31
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.31
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.26
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.23
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.22
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.22
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.22
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.19
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.18
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.17
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.14
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.12
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.09
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.09
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.08
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.07
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.07
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.03
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.01
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.98
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.96
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.96
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.9
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.83
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.81
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.8
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.8
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.78
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.76
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.76
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.74
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.72
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.71
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.71
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.7
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.67
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.65
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.64
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.64
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.63
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.59
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.59
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.58
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.58
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.58
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.55
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.52
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.51
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.5
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.5
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.46
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.45
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.45
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.44
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.44
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.41
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.39
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.39
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.36
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.35
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.34
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.34
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.33
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.3
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.29
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.29
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.29
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.28
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.27
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.27
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.25
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.25
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.25
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.24
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.23
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.22
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.21
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.19
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.17
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.15
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.15
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.15
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.13
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.13
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.12
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.12
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.08
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.07
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.05
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.05
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.03
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.02
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.02
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.02
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.01
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.01
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.01
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.0
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.0
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.0
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.98
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.98
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.97
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.96
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.91
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.9
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.9
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.86
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.85
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.85
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.85
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.81
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.78
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.77
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.7
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.67
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.66
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.65
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.64
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.59
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.56
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.54
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.53
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.51
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.5
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.48
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	97.43
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.43
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.35
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.3
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.28
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.2
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.16
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.16
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.04
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.03
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.02
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.99
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.93
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.92
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.91
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.84
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.76
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.74
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.69
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.69
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.66
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.4
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.36
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.32
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.26
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.24
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.17
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.15
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.09
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.9
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.42
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.19
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	95.15
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.05
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.03
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	94.86
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.23
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.17
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	93.85
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	93.8
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	93.1
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.8
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	92.76
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	92.58
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	91.34
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	89.92
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.23
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	87.21
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	87.14
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	86.99
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	86.49
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	84.71
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	84.46
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	84.41
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	84.11
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	83.54
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	83.05
2p58_C	116	Putative type III secretion protein YSCG; type III	82.8
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	80.92

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=5.8e-34  Score=272.09  Aligned_cols=377  Identities=9%  Similarity=-0.042  Sum_probs=328.0

Q ss_pred             cccccCCChHHHHHHHHHHHHcccchhhHHh---------hhhhHHHHHhhh--CCCChhhHHHHHHHHHhhhccCChHH
Q 040338            2 KACGSLKSLPIARKIHAQLISTCLISSIFLQ---------LIDDDYRVFCDI--GPRYLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         2 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---------~~~~A~~~~~~~--~~~~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      +.|.+.|+++.|..+++++......+..+..         ++++|..+|+++  ..+++.+|+.++.++.+   .|++++
T Consensus        92 ~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~  168 (597)
T 2xpi_A           92 HDALMQQQYKCAAFVGEKVLDITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLYNRSSACRYLAAFCLVK---LYDWQG  168 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGGGTCHHHHHHHHHHHHH---TTCHHH
T ss_pred             HHHHHccCchHHHHHHHHHHhhCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhccccchhHHHHHHHHHHH---HhhHHH
Confidence            3567889999999999999965543322222         899999999998  47889999999999888   899999


Q ss_pred             HHHHHHHHHHh---------------ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcc----------------
Q 040338           71 ALHLHGLVKKF---------------YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLF----------------  119 (385)
Q Consensus        71 a~~~~~~m~~~---------------g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~----------------  119 (385)
                      |.++|+++...               |.+++..+|+.++.+|.+.|++++|.++|++|.+.++.                
T Consensus       169 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~  248 (597)
T 2xpi_A          169 ALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQLVSNHLLTA  248 (597)
T ss_dssp             HHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCSCH
T ss_pred             HHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHHHHhhcccc
Confidence            99999953221               22345789999999999999999999999999654321                


Q ss_pred             ----------------------------------ccccchHHHHHHhcCCCC--CCcchHHHHHHHHHhCCCchHHHHHH
Q 040338          120 ----------------------------------CWKFGIIRLLIMFQKMPE--RDLVSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus       120 ----------------------------------~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                                                        ...|++++|.++|+++..  ++..+|+.++.+|.+.|++++|..+|
T Consensus       249 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  328 (597)
T 2xpi_A          249 DEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAIT  328 (597)
T ss_dssp             HHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHHH
Confidence                                              112889999999999976  88999999999999999999999999


Q ss_pred             HHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------------CCch
Q 040338          164 IELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------------IESS  231 (385)
Q Consensus       164 ~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------------~~~~  231 (385)
                      +++.+.+ +.+..++..++.++.+.|++++|.++++.+.+.. +.+..+++.+...|.+.|+.+            .+.+
T Consensus       329 ~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  406 (597)
T 2xpi_A          329 TKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQF  406 (597)
T ss_dssp             HHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCC
Confidence            9999864 3378889999999999999999999999999764 467889999999999999887            4456


Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhc
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCS  296 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~  296 (385)
                      ..+|+.++.+|.+.|++++|+++|+++.+   ++..+|+.++.+|.+.|++++|++.|            +|+.++..|.
T Consensus       407 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  486 (597)
T 2xpi_A          407 GPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAF  486 (597)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            78999999999999999999999999875   37789999999999999999999999            8999999999


Q ss_pred             ccCChhhHHHHHHHHHhcc------c---hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCCh
Q 040338          297 HSGPVTKGKHYFTAMAKFT------Y---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNT  365 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~------~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~  365 (385)
                      +.|++++|.++|+++.+..      +   ..++..++.+|.+.|++++|.++|+++.+. | +..+|..+..+|.+.|++
T Consensus       487 ~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  566 (597)
T 2xpi_A          487 NKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKKIP  566 (597)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTTCH
T ss_pred             HhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCH
Confidence            9999999999999998762      2   468899999999999999999999998763 4 788999999999999999


Q ss_pred             HHHHHHHHHHHhccccCC
Q 040338          366 KLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~~  383 (385)
                      ++|.+.++++.+.+|.++
T Consensus       567 ~~A~~~~~~~l~~~p~~~  584 (597)
T 2xpi_A          567 GLAITHLHESLAISPNEI  584 (597)
T ss_dssp             HHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHhcCCCCh
Confidence            999999999999988754

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.5e-31  Score=253.80  Aligned_cols=344  Identities=10%  Similarity=-0.043  Sum_probs=267.9

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLR  112 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  112 (385)
                      .+..+...|+.++.+++..|+.++..+.+   .|++++|..+|++|.+.  .|+..++..++.+|.+.|++++|..+|++
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~g~~~~A~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  142 (597)
T 2xpi_A           68 SFLKERNAQNTDSLSREDYLRLWRHDALM---QQQYKCAAFVGEKVLDI--TGNPNDAFWLAQVYCCTGDYARAKCLLTK  142 (597)
T ss_dssp             --------------CHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             ccCCCCCccccchHHHHHHHHHHHHHHHH---ccCchHHHHHHHHHHhh--CCCchHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            45666777887777888889999999777   89999999999998854  56778888899999999999999999998


Q ss_pred             cc--CCCccccc---------cchHHHHHHhcCCCCC-------------------CcchHHHHHHHHHhCCCchHHHHH
Q 040338          113 ML--NPSLFCWK---------FGIIRLLIMFQKMPER-------------------DLVSWNTMISILTRHGFGFETLCT  162 (385)
Q Consensus       113 m~--~~~~~~~~---------~~~~~a~~~~~~~~~~-------------------~~~~~~~li~~~~~~~~~~~a~~~  162 (385)
                      +.  ..+..++.         |++++|.++|+++.+.                   +..+|+.++.+|.+.|++++|.++
T Consensus       143 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  222 (597)
T 2xpi_A          143 EDLYNRSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKEC  222 (597)
T ss_dssp             TCGGGTCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HhccccchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            83  33443333         8899999999865433                   377899999999999999999999


Q ss_pred             HHHHHHCCC----------------------------------------------------------------------C
Q 040338          163 FIELWNHGF----------------------------------------------------------------------G  172 (385)
Q Consensus       163 ~~~m~~~g~----------------------------------------------------------------------~  172 (385)
                      |++|.+.+.                                                                      +
T Consensus       223 ~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  302 (597)
T 2xpi_A          223 YKEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLE  302 (597)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGG
T ss_pred             HHHHHHhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCC
Confidence            998876432                                                                      1


Q ss_pred             CCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------------CCchhhHHHHHHH
Q 040338          173 LSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------------IESSIQIGKALVT  240 (385)
Q Consensus       173 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------------~~~~~~~~~~li~  240 (385)
                      ++..++..++.++.+.|++++|.++|+++.+.++ .+..+++.++.+|.+.|+.+            .+.+..++..++.
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~  381 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGI  381 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHH
Confidence            4555566666666666666666666666666553 25556666666666666554            4456788999999


Q ss_pred             HHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHH
Q 040338          241 MYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGK  305 (385)
Q Consensus       241 ~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~  305 (385)
                      .|.+.|++++|.++|+++.+   .+..+|+.++.+|.+.|++++|+++|            +|..++.+|.+.|++++|.
T Consensus       382 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  461 (597)
T 2xpi_A          382 YYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLAN  461 (597)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999998865   36779999999999999999999988            8899999999999999999


Q ss_pred             HHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-------CCC--cchHHHHHHHHHhcCChHHHHHHHHH
Q 040338          306 HYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-------KPT--CVIWGALLGACCSHYNTKLAELVMRN  374 (385)
Q Consensus       306 ~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~p~--~~~~~~li~~~~~~g~~~~a~~~~~~  374 (385)
                      ++|+++.+..+  ..++..++..|.+.|++++|.++|+++.+       .|+  ..+|..++.+|.+.|++++|.+.+++
T Consensus       462 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  541 (597)
T 2xpi_A          462 EYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQ  541 (597)
T ss_dssp             HHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            99999988776  78899999999999999999999998844       466  67899999999999999999999999


Q ss_pred             HHhccccC
Q 040338          375 LLQLDVKV  382 (385)
Q Consensus       375 ~~~~~~~~  382 (385)
                      +.+.+|..
T Consensus       542 ~~~~~p~~  549 (597)
T 2xpi_A          542 GLLLSTND  549 (597)
T ss_dssp             HHHHSSCC
T ss_pred             HHHhCCCC
Confidence            99887654

>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=99.98  E-value=1e-31  Score=248.23  Aligned_cols=185  Identities=9%  Similarity=0.007  Sum_probs=169.6

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC---------hhHHHHHHHhccCCCcc
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA---------VDYAESAFLRMLNPSLF  119 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~---------~~~a~~~~~~m~~~~~~  119 (385)
                      ...++.+|.+|++   .|++++|+++|++|.+.|+.||..+||+||.+|++.+.         +++|.++|++|.+.|+ 
T Consensus        26 e~~l~~~id~c~k---~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~-  101 (501)
T 4g26_A           26 EALLKQKLDMCSK---KGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKV-  101 (501)
T ss_dssp             HHHHHHHHHHTTT---SCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHh---CCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCC-
Confidence            3457889999666   99999999999999999999999999999999998765         6789999999999998 


Q ss_pred             ccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHH
Q 040338          120 CWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHS  199 (385)
Q Consensus       120 ~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  199 (385)
                                       .||..|||+||.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|+
T Consensus       102 -----------------~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~  164 (501)
T 4g26_A          102 -----------------VPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDA  164 (501)
T ss_dssp             -----------------CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             -----------------CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHH
Confidence                             899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----CChhhHHHHHHHHHh
Q 040338          200 RVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR----RNMISWMVLISAFSQ  275 (385)
Q Consensus       200 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~li~~~~~  275 (385)
                      +|.+.|+.||..+|                      ++||.+|++.|++++|.++|++|.+    |+..||+.++..|+.
T Consensus       165 ~M~~~G~~Pd~~ty----------------------~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          165 HMVESEVVPEEPEL----------------------AALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHHHTTCCCCHHHH----------------------HHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             HHHhcCCCCCHHHH----------------------HHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            99999998887777                      5555556666699999999999985    899999999999986


Q ss_pred             c
Q 040338          276 A  276 (385)
Q Consensus       276 ~  276 (385)
                      .
T Consensus       223 ~  223 (501)
T 4g26_A          223 E  223 (501)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.98  E-value=1.2e-31  Score=247.91  Aligned_cols=174  Identities=8%  Similarity=-0.013  Sum_probs=161.4

Q ss_pred             hhhhHHHHHhhhC----CCChhhHHHHHHHHHhhhc------cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC
Q 040338           33 LIDDDYRVFCDIG----PRYLFTYNTMINGGVRCLC------VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA  102 (385)
Q Consensus        33 ~~~~A~~~~~~~~----~~~~~~~~~li~~~~~~~~------~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~  102 (385)
                      ++++|.++|++|.    +||..|||+||.+|+.+..      .+.+++|.++|++|.+.|+.||..+|++||.+|++.|+
T Consensus        41 ~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~  120 (501)
T 4g26_A           41 DVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDD  120 (501)
T ss_dssp             CHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC
Confidence            6777777777775    7999999999999775321      34478999999999999999999999999999999999


Q ss_pred             hhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHH
Q 040338          103 VDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAF  182 (385)
Q Consensus       103 ~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll  182 (385)
                      +++|.++|++|.+.|+                  .||..+||+||.+|++.|++++|.++|++|.+.|+.||..||++||
T Consensus       121 ~~~A~~l~~~M~~~g~------------------~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li  182 (501)
T 4g26_A          121 PEMAFDMVKQMKAFGI------------------QPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALL  182 (501)
T ss_dssp             HHHHHHHHHHHHHTTC------------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCC------------------CCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            9999999999999998                  8999999999999999999999999999999999999999999999


Q ss_pred             HHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          183 SARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       183 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      .+|++.|++++|.+++++|.+.|..|+..||+.++..|+..+
T Consensus       183 ~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          183 KVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHH
T ss_pred             HHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCc
Confidence            999999999999999999999999999999999999988743

>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=99.95  E-value=1.1e-24  Score=196.75  Aligned_cols=331  Identities=11%  Similarity=0.055  Sum_probs=266.8

Q ss_pred             cccCCChHHHHHHHHHHHHcccchhhHHh----------hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHH
Q 040338            4 CGSLKSLPIARKIHAQLISTCLISSIFLQ----------LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKM   70 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~   70 (385)
                      +-+.|+++.|...+.++.+..........          ++++|...++...   +.+..+|..+...+..   .|++++
T Consensus         9 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~---~g~~~~   85 (388)
T 1w3b_A            9 EYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKE---RGQLQE   85 (388)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---HTCHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHH---CCCHHH
Confidence            34578999999999888876533322221          7788888887554   4456778888888777   789999


Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHH
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISIL  150 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  150 (385)
                      |...|+++.+.. +.+..+|..+..++.+.|++++|.+.|+++.+.+                   +.+...+..+...+
T Consensus        86 A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~~l~~~~  145 (388)
T 1w3b_A           86 AIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-------------------PDLYCVRSDLGNLL  145 (388)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-------------------TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCcHHHHHHHHHHH
Confidence            999998888763 3345678888888888999999998888876544                   23455677778888


Q ss_pred             HhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCC
Q 040338          151 TRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIE  229 (385)
Q Consensus       151 ~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~  229 (385)
                      ...|++++|.+.|+++.+.  .| +..+|..+...+.+.|++++|...++++.+.++                       
T Consensus       146 ~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-----------------------  200 (388)
T 1w3b_A          146 KALGRLEEAKACYLKAIET--QPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP-----------------------  200 (388)
T ss_dssp             HTTSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT-----------------------
T ss_pred             HHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-----------------------
Confidence            8889999999999888875  34 567888888888889999999999988887653                       


Q ss_pred             chhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHH
Q 040338          230 SSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSG  294 (385)
Q Consensus       230 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~  294 (385)
                      .+...+..+...+...|++++|+..|++..+  | +..++..+..+|.+.|++++|++.+            +|..+...
T Consensus       201 ~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  280 (388)
T 1w3b_A          201 NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANA  280 (388)
T ss_dssp             TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHH
Confidence            1234556777778888899999998887764  3 5678888888999999999998888            78889999


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHH
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      +.+.|++++|...++++.+..+  ...+..+...+.+.|++++|.+.++++.+. | +..+|..+...|.+.|++++|..
T Consensus       281 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~  360 (388)
T 1w3b_A          281 LKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALM  360 (388)
T ss_dssp             HHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            9999999999999999998877  788899999999999999999999999874 4 46689999999999999999999


Q ss_pred             HHHHHHhccccC
Q 040338          371 VMRNLLQLDVKV  382 (385)
Q Consensus       371 ~~~~~~~~~~~~  382 (385)
                      .++++.+..|..
T Consensus       361 ~~~~a~~~~p~~  372 (388)
T 1w3b_A          361 HYKEAIRISPTF  372 (388)
T ss_dssp             HHHHHHTTCTTC
T ss_pred             HHHHHHhhCCCC
Confidence            999999887754

>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=99.92  E-value=1.9e-22  Score=182.13  Aligned_cols=302  Identities=10%  Similarity=0.007  Sum_probs=257.1

Q ss_pred             hhhhHHHHHhhhC--CCCh-hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG--PRYL-FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~-~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|...|+.+.  .|+. ..+..+...+..   .|++++|...++...+.. +.+..+|..+..+|.+.|++++|.+.
T Consensus        14 ~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~---~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   89 (388)
T 1w3b_A           14 DFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQ---CRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEH   89 (388)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHH
Confidence            7899999998765  4544 344444444444   899999999999988764 55788999999999999999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-HhhHHHHHHHhcCc
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS-SMLYATAFSARASV  188 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~  188 (385)
                      |+++.+.+                   +.+..+|..+..++.+.|++++|.+.|+++.+.  .|+ ...+..+...+...
T Consensus        90 ~~~al~~~-------------------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~  148 (388)
T 1w3b_A           90 YRHALRLK-------------------PDFIDGYINLAAALVAAGDMEGAVQAYVSALQY--NPDLYCVRSDLGNLLKAL  148 (388)
T ss_dssp             HHHHHHHC-------------------TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH--CTTCTHHHHHHHHHHHTT
T ss_pred             HHHHHHcC-------------------cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHc
Confidence            99886544                   345668999999999999999999999999875  464 44566788888999


Q ss_pred             cCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-Chhh
Q 040338          189 YDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMIS  265 (385)
Q Consensus       189 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~  265 (385)
                      |++++|.+.++.+.+..+                       .+..+|..+...+.+.|++++|+..|+++.+  | +...
T Consensus       149 g~~~~A~~~~~~al~~~p-----------------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  205 (388)
T 1w3b_A          149 GRLEEAKACYLKAIETQP-----------------------NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDA  205 (388)
T ss_dssp             SCHHHHHHHHHHHHHHCT-----------------------TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             cCHHHHHHHHHHHHHhCC-----------------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHH
Confidence            999999999999988743                       2344567788888899999999999999976  3 5678


Q ss_pred             HHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC
Q 040338          266 WMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG  331 (385)
Q Consensus       266 ~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g  331 (385)
                      |..+...+...|++++|+..+            ++..+...+...|++++|...++++.+..+  +..+..+...+.+.|
T Consensus       206 ~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g  285 (388)
T 1w3b_A          206 YINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKG  285 (388)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcC
Confidence            889999999999999999988            888999999999999999999999999877  788999999999999


Q ss_pred             CHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          332 LLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       332 ~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ++++|.+.|+++.+.  ++..+|..+...+...|++++|...++++.+..|..
T Consensus       286 ~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  338 (388)
T 1w3b_A          286 SVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEF  338 (388)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTC
T ss_pred             CHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCc
Confidence            999999999998763  467789999999999999999999999999887653

>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=99.89  E-value=4.7e-21  Score=176.25  Aligned_cols=287  Identities=10%  Similarity=-0.031  Sum_probs=236.9

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      +...|..+...+..   .|++++|..+|+.+.+.. +.+..++..+..+|...|++++|...|+++.+.+          
T Consensus        25 ~~~~~~~~~~~~~~---~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~----------   90 (450)
T 2y4t_A           25 DVEKHLELGKKLLA---AGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK----------   90 (450)
T ss_dssp             HHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             HHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----------
Confidence            45677888888777   899999999999999864 4578899999999999999999999999987655          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH----hhHHHH------------HHHhcCccCc
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS----MLYATA------------FSARASVYDL  191 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~l------------l~~~~~~~~~  191 (385)
                               +.+..++..+..+|.+.|++++|...|+++.+.  .|+.    ..+..+            ...+.+.|++
T Consensus        91 ---------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  159 (450)
T 2y4t_A           91 ---------MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDY  159 (450)
T ss_dssp             ---------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCH
T ss_pred             ---------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence                     356788999999999999999999999999875  4543    444444            3448889999


Q ss_pred             cchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHH
Q 040338          192 EWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMV  268 (385)
Q Consensus       192 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~  268 (385)
                      ++|...++.+.+..+ .                      +..++..+...|.+.|++++|+..|+++.+   .+..++..
T Consensus       160 ~~A~~~~~~~~~~~~-~----------------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  216 (450)
T 2y4t_A          160 TAAIAFLDKILEVCV-W----------------------DAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYK  216 (450)
T ss_dssp             HHHHHHHHHHHHHCT-T----------------------CHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHH
T ss_pred             HHHHHHHHHHHHhCC-C----------------------ChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            999999999988753 2                      334456667777777788888888887764   35677888


Q ss_pred             HHHHHHhcCCCCchHHHH------------HHHH------------HHHHhcccCChhhHHHHHHHHHhccc------hh
Q 040338          269 LISAFSQAGVLEKPRFFF------------FFVS------------LLSGCSHSGPVTKGKHYFTAMAKFTY------TC  318 (385)
Q Consensus       269 li~~~~~~g~~~~a~~~~------------~~~~------------l~~~~~~~~~~~~a~~~~~~~~~~~~------~~  318 (385)
                      +...|...|++++|+..+            .+..            +...|.+.|++++|...++.+.+..+      ..
T Consensus       217 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~  296 (450)
T 2y4t_A          217 ISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVR  296 (450)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHH
Confidence            888888888888888877            3333            37889999999999999999988766      23


Q ss_pred             hHHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          319 YFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       319 ~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .+..+...+.+.|++++|...++++.. .| +...|..+..+|...|++++|...++++.+..|..
T Consensus       297 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~  362 (450)
T 2y4t_A          297 SKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNEND  362 (450)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcch
Confidence            678889999999999999999999865 34 67889999999999999999999999999988765

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.88  E-value=7.3e-21  Score=177.85  Aligned_cols=344  Identities=10%  Similarity=-0.053  Sum_probs=268.0

Q ss_pred             hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHH
Q 040338           33 LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF  110 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~  110 (385)
                      ++++|...|+++.  .|+...|..+..++..   .|++++|...++.+.+.+ +.+..++..+..+|.+.|++++|...|
T Consensus        21 ~~~~A~~~~~~al~~~p~~~~~~~la~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~   96 (514)
T 2gw1_A           21 KYDDAIKYYNWALELKEDPVFYSNLSACYVS---VGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFDL   96 (514)
T ss_dssp             CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcCccHHHHHhHHHHHHH---HhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            5666666666554  5788888888888777   899999999999998875 346678888999999999999999999


Q ss_pred             HhccCCCcccccc------------chHHH--------------------------------------HHHhcCCC----
Q 040338          111 LRMLNPSLFCWKF------------GIIRL--------------------------------------LIMFQKMP----  136 (385)
Q Consensus       111 ~~m~~~~~~~~~~------------~~~~a--------------------------------------~~~~~~~~----  136 (385)
                      +++.+.+......            ....+                                      ...+....    
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  176 (514)
T 2gw1_A           97 SVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELT  176 (514)
T ss_dssp             HHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCC
T ss_pred             HHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHH
Confidence            8886554321110            00000                                      00000000    


Q ss_pred             -----CC-CcchHHHHHHHHHh---CCCchHHHHHHHHHHH-----CCCC-------C-CHhhHHHHHHHhcCccCccch
Q 040338          137 -----ER-DLVSWNTMISILTR---HGFGFETLCTFIELWN-----HGFG-------L-SSMLYATAFSARASVYDLEWG  194 (385)
Q Consensus       137 -----~~-~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~-----~g~~-------p-~~~t~~~ll~~~~~~~~~~~a  194 (385)
                           .| +...+..+...+..   .|++++|..+|+++.+     ..-.       | +..++..+...+...|++++|
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A  256 (514)
T 2gw1_A          177 FANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGA  256 (514)
T ss_dssp             CSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHH
Confidence                 01 13333334444443   7899999999999887     3112       2 355677788888899999999


Q ss_pred             hhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--
Q 040338          195 PHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--  260 (385)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--  260 (385)
                      ...++.+.+..+.  ..++..+...|...|+.+            .+.+..++..+...+...|++++|...|++..+  
T Consensus       257 ~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  334 (514)
T 2gw1_A          257 HEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELD  334 (514)
T ss_dssp             HHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTC
T ss_pred             HHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            9999999988755  888888999999999887            445677889999999999999999999998865  


Q ss_pred             -CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hh------h
Q 040338          261 -RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TC------Y  319 (385)
Q Consensus       261 -~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~------~  319 (385)
                       .+...+..+...+...|++++|+..+            ++..+...+...|++++|...++++.+..+  ..      .
T Consensus       335 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  414 (514)
T 2gw1_A          335 PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAP  414 (514)
T ss_dssp             SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHH
Confidence             35678889999999999999999998            788899999999999999999999988766  22      8


Q ss_pred             HHHHHHHHHc---cCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          320 FVCMVDLLGL---SGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       320 ~~~li~~~~~---~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +..+...+..   .|++++|.+.|+.+... | +..++..+...|...|++++|...+++..+.+|..
T Consensus       415 ~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  482 (514)
T 2gw1_A          415 LVGKATLLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEESADLARTM  482 (514)
T ss_dssp             HHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSH
T ss_pred             HHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhcccc
Confidence            8899999999   99999999999988653 3 56688899999999999999999999999988764

>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=99.88  E-value=7.6e-20  Score=168.18  Aligned_cols=302  Identities=10%  Similarity=-0.004  Sum_probs=242.0

Q ss_pred             hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|..+|+++.   +.+..+|..+...+..   .|++++|...++.+.+.+ +.+..++..+..+|.+.|++++|.+.
T Consensus        41 ~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~  116 (450)
T 2y4t_A           41 QLADALSQFHAAVDGDPDNYIAYYRRATVFLA---MGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDD  116 (450)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH---CCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            8888888888765   4567888888888777   899999999999999875 34678999999999999999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCc---chHHHHH------------HHHHhCCCchHHHHHHHHHHHCCCCCC
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDL---VSWNTMI------------SILTRHGFGFETLCTFIELWNHGFGLS  174 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~li------------~~~~~~~~~~~a~~~~~~m~~~g~~p~  174 (385)
                      |+++.+.+                   +.+.   ..+..+.            ..+.+.|++++|+..|+++.+. .+.+
T Consensus       117 ~~~~~~~~-------------------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~~~~  176 (450)
T 2y4t_A          117 FKKVLKSN-------------------PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEV-CVWD  176 (450)
T ss_dssp             HHHHHTSC-------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-CTTC
T ss_pred             HHHHHhcC-------------------CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCC
Confidence            99987765                   2344   5555553            4488999999999999999875 2346


Q ss_pred             HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHH
Q 040338          175 SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLA  254 (385)
Q Consensus       175 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  254 (385)
                      ..++..+..++.+.|++++|.+.++.+.+..+                       .+..++..+...|...|++++|+..
T Consensus       177 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-----------------------~~~~~~~~l~~~~~~~g~~~~A~~~  233 (450)
T 2y4t_A          177 AELRELRAECFIKEGEPRKAISDLKAASKLKN-----------------------DNTEAFYKISTLYYQLGDHELSLSE  233 (450)
T ss_dssp             HHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHC-----------------------SCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-----------------------CCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            78889999999999999999999999987642                       2344567777888888899999999


Q ss_pred             HHhccc--C-ChhhHHHH------------HHHHHhcCCCCchHHHH----------------HHHHHHHHhcccCChhh
Q 040338          255 FELMSR--R-NMISWMVL------------ISAFSQAGVLEKPRFFF----------------FFVSLLSGCSHSGPVTK  303 (385)
Q Consensus       255 ~~~m~~--~-~~~~~~~l------------i~~~~~~g~~~~a~~~~----------------~~~~l~~~~~~~~~~~~  303 (385)
                      |+++.+  | +...+..+            ...+.+.|++++|+..+                .+..+...+.+.|++++
T Consensus       234 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~  313 (450)
T 2y4t_A          234 VRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVE  313 (450)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHH
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHH
Confidence            998865  3 33444444            78888999999999888                57788899999999999


Q ss_pred             HHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHH------------HHHhcC----
Q 040338          304 GKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLG------------ACCSHY----  363 (385)
Q Consensus       304 a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~------------~~~~~g----  363 (385)
                      |...++++.+..+  ...+..+..+|...|++++|.+.|+++.+. |+ ...+..+..            .|...|    
T Consensus       314 A~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~  393 (450)
T 2y4t_A          314 AIRVCSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRN  393 (450)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTT
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHhhcccchhHHHHhCCCcc
Confidence            9999999988766  888999999999999999999999998764 54 445555552            233344    


Q ss_pred             -ChHHHHHHHHH-HHhcccc
Q 040338          364 -NTKLAELVMRN-LLQLDVK  381 (385)
Q Consensus       364 -~~~~a~~~~~~-~~~~~~~  381 (385)
                       +.+++.+.+++ ..+..|.
T Consensus       394 ~~~~~~~~~y~~~~l~~~pd  413 (450)
T 2y4t_A          394 AKKQEIIKAYRKLALQWHPD  413 (450)
T ss_dssp             CCTTHHHHHHHHHHHHSCGG
T ss_pred             CCHHHHHHHHHHHHHHhCCC
Confidence             55677888876 5555554

>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=99.84  E-value=6.6e-19  Score=165.58  Aligned_cols=321  Identities=9%  Similarity=-0.007  Sum_probs=227.4

Q ss_pred             hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|...|+++.   +.++..|..+...+..   .|++++|.+.++++.+.+ +.+..++..+..+|...|++++|.+.
T Consensus        40 ~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~  115 (537)
T 3fp2_A           40 NFNEAIKYYQYAIELDPNEPVFYSNISACYIS---TGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTDAMFD  115 (537)
T ss_dssp             CCC-CHHHHHHHHHHCTTCHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHH---cCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            7777777777654   3456777777777666   788888888888888765 34677788888888888888888888


Q ss_pred             HHhccCCCcccc--------c-----------------------------------------------------------
Q 040338          110 FLRMLNPSLFCW--------K-----------------------------------------------------------  122 (385)
Q Consensus       110 ~~~m~~~~~~~~--------~-----------------------------------------------------------  122 (385)
                      |+.+........        .                                                           
T Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (537)
T 3fp2_A          116 LSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYAL  195 (537)
T ss_dssp             HHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHH
T ss_pred             HHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHH
Confidence            854421110000        0                                                           


Q ss_pred             --------------------cchHHHHHHhcCCCC--CC--------cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCC
Q 040338          123 --------------------FGIIRLLIMFQKMPE--RD--------LVSWNTMISILTRHGFGFETLCTFIELWNHGFG  172 (385)
Q Consensus       123 --------------------~~~~~a~~~~~~~~~--~~--------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  172 (385)
                                          +++++|...|.++..  |+        ..++..+...+...|++++|...|++..+.  .
T Consensus       196 ~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~  273 (537)
T 3fp2_A          196 LSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINL--H  273 (537)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C
T ss_pred             HHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc--C
Confidence                                244455555544422  21        113444445555566666666666666553  3


Q ss_pred             CCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHH
Q 040338          173 LSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKAD  252 (385)
Q Consensus       173 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~  252 (385)
                      |+...+..+...+...|++++|...++.+.+..                       +.+..++..+...+...|++++|+
T Consensus       274 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-----------------------~~~~~~~~~l~~~~~~~~~~~~A~  330 (537)
T 3fp2_A          274 PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-----------------------PEYPPTYYHRGQMYFILQDYKNAK  330 (537)
T ss_dssp             CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-----------------------TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-----------------------CCCHHHHHHHHHHHHhcCCHHHHH
Confidence            445555555566666666666666666655543                       234556778888888899999999


Q ss_pred             HHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-
Q 040338          253 LAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-  316 (385)
Q Consensus       253 ~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-  316 (385)
                      ..|++..+  | +...+..+...+...|++++|+..+            .+..+...+...|++++|...++++.+..+ 
T Consensus       331 ~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~  410 (537)
T 3fp2_A          331 EDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEV  410 (537)
T ss_dssp             HHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCc
Confidence            99998875  3 5678889999999999999999998            888899999999999999999999888766 


Q ss_pred             -------hhhHHHHHHHHHcc----------CCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          317 -------TCYFVCMVDLLGLS----------GLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       317 -------~~~~~~li~~~~~~----------g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                             ...+......+.+.          |++++|...|++..+. | +...|..+...|...|++++|...+++..+
T Consensus       411 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  490 (537)
T 3fp2_A          411 QEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAI  490 (537)
T ss_dssp             CSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence                   12234445677777          9999999999988763 4 567889999999999999999999999998


Q ss_pred             ccccC
Q 040338          378 LDVKV  382 (385)
Q Consensus       378 ~~~~~  382 (385)
                      ..|..
T Consensus       491 ~~~~~  495 (537)
T 3fp2_A          491 LARTM  495 (537)
T ss_dssp             HC--C
T ss_pred             hCCCc
Confidence            87764

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.84  E-value=6.2e-19  Score=164.72  Aligned_cols=307  Identities=8%  Similarity=-0.107  Sum_probs=251.3

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHH
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIM  131 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~  131 (385)
                      |...-..+..   .|++++|...|+++.+..  |+..+|..+..+|.+.|++++|.+.|+++.+.+              
T Consensus         9 ~~~~g~~~~~---~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--------------   69 (514)
T 2gw1_A            9 LKDKGNQFFR---NKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK--------------   69 (514)
T ss_dssp             HHHHHHHHHH---TSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--------------
T ss_pred             HHHHHHHHHH---hccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC--------------
Confidence            3444445445   899999999999999975  789999999999999999999999999887655              


Q ss_pred             hcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-------------------------------------
Q 040338          132 FQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS-------------------------------------  174 (385)
Q Consensus       132 ~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-------------------------------------  174 (385)
                           +.+..+|..+..++.+.|++++|...|+++.+.+...+                                     
T Consensus        70 -----p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  144 (514)
T 2gw1_A           70 -----PDYSKVLLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELS  144 (514)
T ss_dssp             -----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------
T ss_pred             -----hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Confidence                 35677899999999999999999999999877642100                                     


Q ss_pred             -----------------------------------------HhhHHHHHHHhc---CccCccchhhHHHHHHH-----hC
Q 040338          175 -----------------------------------------SMLYATAFSARA---SVYDLEWGPHLHSRVVH-----ME  205 (385)
Q Consensus       175 -----------------------------------------~~t~~~ll~~~~---~~~~~~~a~~~~~~~~~-----~~  205 (385)
                                                               ...+......+.   +.|++++|...++.+.+     ..
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~  224 (514)
T 2gw1_A          145 TQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLD  224 (514)
T ss_dssp             ------------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CChhhHHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhc
Confidence                                                     222222222222   48999999999999988     31


Q ss_pred             C--------CCchHHHHHHHHHHHhcCCCC-----------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CCh
Q 040338          206 P--------SLDVFVGSGLIDMYLKCGCNG-----------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNM  263 (385)
Q Consensus       206 ~--------~~~~~~~~~li~~~~~~g~~~-----------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~  263 (385)
                      .        +.+..++..+...+...|+.+           ..|+..++..+...+...|++++|...++...+   .+.
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  304 (514)
T 2gw1_A          225 KNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNS  304 (514)
T ss_dssp             TSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCT
T ss_pred             cCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCH
Confidence            1        234567778888888888776           334488889999999999999999999998876   366


Q ss_pred             hhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHc
Q 040338          264 ISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGL  329 (385)
Q Consensus       264 ~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~  329 (385)
                      ..+..+...|...|++++|+..+            ++..+...+...|++++|...++.+.+..+  ...+..+...+.+
T Consensus       305 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~  384 (514)
T 2gw1_A          305 SVYYHRGQMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTD  384 (514)
T ss_dssp             HHHHHHHHHHHHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHH
Confidence            78889999999999999999998            788899999999999999999999988776  7788889999999


Q ss_pred             cCCHHHHHHHHHhCCCC-C---C----cchHHHHHHHHHh---cCChHHHHHHHHHHHhccccC
Q 040338          330 SGLLGEAKKLIDEMPSK-P---T----CVIWGALLGACCS---HYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       330 ~g~~~~A~~~~~~m~~~-p---~----~~~~~~li~~~~~---~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .|++++|.+.++++... |   +    ...|..+...|..   .|++++|...++++.+..+..
T Consensus       385 ~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~  448 (514)
T 2gw1_A          385 KNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPRS  448 (514)
T ss_dssp             TTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTC
T ss_pred             CCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCccc
Confidence            99999999999988653 2   2    3388999999999   999999999999998877654

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.82  E-value=4.4e-18  Score=151.14  Aligned_cols=286  Identities=10%  Similarity=-0.031  Sum_probs=233.6

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      +..+..+-..+..   .|++++|...++.+.+.. +.+..++..+...+...|++++|...|+++.+.+           
T Consensus         3 ~~~~~~~~~~~~~---~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-----------   67 (359)
T 3ieg_A            3 VEKHLELGKKLLA---AGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-----------   67 (359)
T ss_dssp             HHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHHHHHHHH---cCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-----------
Confidence            4455566666555   899999999999999874 4467899999999999999999999998876544           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC----CHhhHHHH------------HHHhcCccCcc
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL----SSMLYATA------------FSARASVYDLE  192 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p----~~~t~~~l------------l~~~~~~~~~~  192 (385)
                              +.+...|..+...+...|++++|...|++..+.  .|    +...+..+            ...+...|+++
T Consensus        68 --------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  137 (359)
T 3ieg_A           68 --------MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYT  137 (359)
T ss_dssp             --------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             --------CCcchHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHH
Confidence                    346678999999999999999999999999875  45    33344333            47788999999


Q ss_pred             chhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHH
Q 040338          193 WGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVL  269 (385)
Q Consensus       193 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~l  269 (385)
                      +|.+.++.+.+..+.                       +...+..+...+...|++++|...+++..+   .+..++..+
T Consensus       138 ~A~~~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l  194 (359)
T 3ieg_A          138 AAITFLDKILEVCVW-----------------------DAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKI  194 (359)
T ss_dssp             HHHHHHHHHHHHCTT-----------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC-----------------------chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            999999999887542                       233456677777888899999999988875   366788888


Q ss_pred             HHHHHhcCCCCchHHHH------------HH------------HHHHHHhcccCChhhHHHHHHHHHhccc------hhh
Q 040338          270 ISAFSQAGVLEKPRFFF------------FF------------VSLLSGCSHSGPVTKGKHYFTAMAKFTY------TCY  319 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~------------~~------------~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~  319 (385)
                      ...+...|++++|...+            .+            ..+...+...|++++|...++++.+..+      ...
T Consensus       195 a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~  274 (359)
T 3ieg_A          195 STLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRS  274 (359)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHH
Confidence            88899999999998888            22            2336678899999999999999988776      234


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +..+...+...|++++|.+.+++..+ .| +..+|..+...|...|++++|...+++..+.+|..
T Consensus       275 ~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~  339 (359)
T 3ieg_A          275 KERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNEND  339 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTC
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC
Confidence            55688899999999999999998876 34 67789999999999999999999999999988764

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.82  E-value=3.2e-21  Score=183.97  Aligned_cols=149  Identities=16%  Similarity=0.127  Sum_probs=119.3

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHH---HhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVK---KFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~---~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                      .|||+||.+||+   .|++++|.++|++|.   +.|+.||+.|||+||++||+.|++++|.++|++|.+.|+        
T Consensus       128 ~TynaLIdglcK---~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~--------  196 (1134)
T 3spa_A          128 QRLLAFFKCCLL---TDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGL--------  196 (1134)
T ss_dssp             HHHHHHHHHHHH---HTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTC--------
T ss_pred             HHHHHHHHHHHh---CCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCC--------
Confidence            589999999888   799999999998876   458999999999999999999999999999999999998        


Q ss_pred             HHHHHhcCCCCCCcchHHHHHHHHHhCCCc-hHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          127 RLLIMFQKMPERDLVSWNTMISILTRHGFG-FETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       127 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                                .||+.|||+||.++++.|+. ++|.++|++|.+.|+.||..||+.++.++.+.+-+    +..+.+ .-+
T Consensus       197 ----------~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL----~~Vrkv-~P~  261 (1134)
T 3spa_A          197 ----------TPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVL----KAVHKV-KPT  261 (1134)
T ss_dssp             ----------CCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHH----HHHGGG-CCC
T ss_pred             ----------CCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHH----HHHHHh-Ccc
Confidence                      89999999999999999985 68899999999999999999999888655543322    222222 223


Q ss_pred             CCCc------hHHHHHHHHHHHhcC
Q 040338          206 PSLD------VFVGSGLIDMYLKCG  224 (385)
Q Consensus       206 ~~~~------~~~~~~li~~~~~~g  224 (385)
                      +.|+      ..+...|.+.|.+.+
T Consensus       262 f~p~~~~~~~~~t~~LL~dl~s~d~  286 (1134)
T 3spa_A          262 FSLPPQLPPPVNTSKLLRDVYAKDG  286 (1134)
T ss_dssp             CCCCCCCCCCCCCCTTTHHHHCCCS
T ss_pred             cCCCCCCcccccchHHHHHHHccCC
Confidence            4443      344444555565555

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.81  E-value=2.5e-20  Score=177.89  Aligned_cols=142  Identities=12%  Similarity=0.055  Sum_probs=119.6

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccC---CCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLN---PSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                      ..|||+||++||+.|++++|.++|++|.+   .|+                  .||+.|||+||.+||+.|++++|.++|
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~------------------~PdvvTYNtLI~Glck~G~~~eA~~Lf  188 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRK------------------LLTLDMYNAVMLGWARQGAFKELVYVL  188 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHT------------------TCCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCC------------------CCCHhHHHHHHHHHHhCCCHHHHHHHH
Confidence            46899999999999999999999988754   355                  799999999999999999999999999


Q ss_pred             HHHHHCCCCCCHhhHHHHHHHhcCccCc-cchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC--------CCCCCc----
Q 040338          164 IELWNHGFGLSSMLYATAFSARASVYDL-EWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG--------CNGIES----  230 (385)
Q Consensus       164 ~~m~~~g~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g--------~~~~~~----  230 (385)
                      ++|.+.|+.||..||+++|.++++.|+. ++|.++|++|.+.|+.||..+|++++....+.+        +.+..|    
T Consensus       189 ~eM~~~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p~~~~  268 (1134)
T 3spa_A          189 FMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQL  268 (1134)
T ss_dssp             HHHHHTTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCCCC
T ss_pred             HHHHHcCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCcccCCCCCC
Confidence            9999999999999999999999999985 789999999999999999999996555544443        333222    


Q ss_pred             --hhhHHHHHHHHHHcCC
Q 040338          231 --SIQIGKALVTMYAEGG  246 (385)
Q Consensus       231 --~~~~~~~li~~~~~~g  246 (385)
                        .+.+...|.+.|.+.+
T Consensus       269 ~~~~~t~~LL~dl~s~d~  286 (1134)
T 3spa_A          269 PPPVNTSKLLRDVYAKDG  286 (1134)
T ss_dssp             CCCCCCCTTTHHHHCCCS
T ss_pred             cccccchHHHHHHHccCC
Confidence              2445555666666544

>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=99.79  E-value=1.1e-16  Score=140.60  Aligned_cols=271  Identities=10%  Similarity=-0.040  Sum_probs=178.2

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      ++..+..+...+..   .|++++|.++++.+.+.. +.+...+..++..+.+.|++++|..+++++.+.+          
T Consensus        21 ~~~~~~~~a~~~~~---~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~----------   86 (330)
T 3hym_B           21 NLDVVVSLAERHYY---NCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY----------   86 (330)
T ss_dssp             CCTTHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC----------
T ss_pred             hHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC----------
Confidence            44445555555544   677777777777777654 3355566666677777777777777777765443          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCC-CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHG-FGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                               +.+..+|..+...+...| ++++|...|++..+.. +.+...+..+...+...|++++|.+.++...+...
T Consensus        87 ---------~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~  156 (330)
T 3hym_B           87 ---------PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK  156 (330)
T ss_dssp             ---------TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT
T ss_pred             ---------cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc
Confidence                     345566777777777777 7777777777776542 22455666777777777777777777777776643


Q ss_pred             CCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchH
Q 040338          207 SLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       207 ~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~  283 (385)
                      .                       +...+..+...+...|++++|...+++..+   .+...+..+...+...|++++|+
T Consensus       157 ~-----------------------~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~  213 (330)
T 3hym_B          157 G-----------------------CHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAE  213 (330)
T ss_dssp             T-----------------------CSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             c-----------------------cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHH
Confidence            2                       112234455566666677777777776654   24455666666666666666666


Q ss_pred             HHH---------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHH
Q 040338          284 FFF---------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLI  340 (385)
Q Consensus       284 ~~~---------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~  340 (385)
                      ..+                     ++..+...+...|++++|...+++..+..+  ...+..+...+.+.|++++|.+.|
T Consensus       214 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  293 (330)
T 3hym_B          214 KWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYF  293 (330)
T ss_dssp             HHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHH
Confidence            555                     455666777777778888888888777666  677777888888888888888888


Q ss_pred             HhCCCC-C-CcchHHHHHHHH-HhcCCh
Q 040338          341 DEMPSK-P-TCVIWGALLGAC-CSHYNT  365 (385)
Q Consensus       341 ~~m~~~-p-~~~~~~~li~~~-~~~g~~  365 (385)
                      ++..+. | +...+..+..++ ...|+.
T Consensus       294 ~~al~~~p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          294 HTALGLRRDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             HTTTTTCSCCHHHHHHHHHHHHTTTTC-
T ss_pred             HHHHccCCCchHHHHHHHHHHHHHhCch
Confidence            887764 4 455666666666 444544

>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=99.78  E-value=1.2e-17  Score=146.68  Aligned_cols=257  Identities=10%  Similarity=-0.044  Sum_probs=219.2

Q ss_pred             cCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHH
Q 040338           83 FVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCT  162 (385)
Q Consensus        83 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  162 (385)
                      .+.+...+..+...+...|++++|.++|+++.+.+                   +.+...+..++..+...|++++|..+
T Consensus        18 ~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-------------------p~~~~~~~~~~~~~~~~~~~~~A~~~   78 (330)
T 3hym_B           18 LQENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-------------------PFHASCLPVHIGTLVELNKANELFYL   78 (330)
T ss_dssp             --CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCTTTHHHHHHHHHHHTCHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------------------CCChhhHHHHHHHHHHhhhHHHHHHH
Confidence            46677888899999999999999999999987655                   35667788888999999999999999


Q ss_pred             HHHHHHCCCCCCHhhHHHHHHHhcCcc-CccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHH
Q 040338          163 FIELWNHGFGLSSMLYATAFSARASVY-DLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTM  241 (385)
Q Consensus       163 ~~~m~~~g~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~  241 (385)
                      ++++.+.. +.+...+..+...+...| ++++|.+.++...+..+.                       +...|..+...
T Consensus        79 ~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~-----------------------~~~~~~~l~~~  134 (330)
T 3hym_B           79 SHKLVDLY-PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKT-----------------------YGPAWIAYGHS  134 (330)
T ss_dssp             HHHHHHHC-TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCTT-----------------------CTHHHHHHHHH
T ss_pred             HHHHHHhC-cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCc-----------------------cHHHHHHHHHH
Confidence            99998852 235677888888999999 999999999999876532                       23345677778


Q ss_pred             HHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHH
Q 040338          242 YAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKH  306 (385)
Q Consensus       242 ~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~  306 (385)
                      +...|++++|+..|++..+  | +...+..+...|...|++++|+..+            .+..+...+...|++++|..
T Consensus       135 ~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~  214 (330)
T 3hym_B          135 FAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEK  214 (330)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHH
Confidence            8888899999999998875  3 4577888999999999999999999            88899999999999999999


Q ss_pred             HHHHHHhcc---------c--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHH
Q 040338          307 YFTAMAKFT---------Y--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMR  373 (385)
Q Consensus       307 ~~~~~~~~~---------~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~  373 (385)
                      .++++.+..         .  ...+..+...|.+.|++++|.+.+++..+.  .+...|..+...|...|++++|...++
T Consensus       215 ~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  294 (330)
T 3hym_B          215 WFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFH  294 (330)
T ss_dssp             HHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHH
Confidence            999998864         2  668889999999999999999999988763  456789999999999999999999999


Q ss_pred             HHHhccccC
Q 040338          374 NLLQLDVKV  382 (385)
Q Consensus       374 ~~~~~~~~~  382 (385)
                      +..+..|..
T Consensus       295 ~al~~~p~~  303 (330)
T 3hym_B          295 TALGLRRDD  303 (330)
T ss_dssp             TTTTTCSCC
T ss_pred             HHHccCCCc
Confidence            999888764

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.78  E-value=1.6e-16  Score=141.01  Aligned_cols=285  Identities=9%  Similarity=-0.028  Sum_probs=218.8

Q ss_pred             hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|...|+++.   +.+...|..+...+..   .|++++|...++.+.+.. +.+...+..+..+|...|++++|...
T Consensus        18 ~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~   93 (359)
T 3ieg_A           18 QLADALSQFHAAVDGDPDNYIAYYRRATVFLA---MGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKLDEAEDD   93 (359)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHhhCcccHHHHHHHHHHHHH---ccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCChHHHHHH
Confidence            4555555555443   3456677777777666   899999999999999874 33678899999999999999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHH------------HHHHHhCCCchHHHHHHHHHHHCCCCCCHhh
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTM------------ISILTRHGFGFETLCTFIELWNHGFGLSSML  177 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l------------i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t  177 (385)
                      |++..+.++..                ..+...+..+            ...+...|++++|..+++++.+. .+.+...
T Consensus        94 ~~~~~~~~~~~----------------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~  156 (359)
T 3ieg_A           94 FKKVLKSNPSE----------------QEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEV-CVWDAEL  156 (359)
T ss_dssp             HHHHHTSCCCH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHH
T ss_pred             HHHHHhcCCcc----------------cChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CCCchHH
Confidence            99987654100                0233444444            57888999999999999999875 2346778


Q ss_pred             HHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHh
Q 040338          178 YATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFEL  257 (385)
Q Consensus       178 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  257 (385)
                      +..+...+...|++++|...++.+.+..+ .                      +..++..+...+...|++++|...|+.
T Consensus       157 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~----------------------~~~~~~~la~~~~~~~~~~~A~~~~~~  213 (359)
T 3ieg_A          157 RELRAECFIKEGEPRKAISDLKAASKLKS-D----------------------NTEAFYKISTLYYQLGDHELSLSEVRE  213 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCS-C----------------------CHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCC-C----------------------CHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            88899999999999999999999987643 1                      233456677777778899999999988


Q ss_pred             ccc--C-ChhhHH------------HHHHHHHhcCCCCchHHHH----------------HHHHHHHHhcccCChhhHHH
Q 040338          258 MSR--R-NMISWM------------VLISAFSQAGVLEKPRFFF----------------FFVSLLSGCSHSGPVTKGKH  306 (385)
Q Consensus       258 m~~--~-~~~~~~------------~li~~~~~~g~~~~a~~~~----------------~~~~l~~~~~~~~~~~~a~~  306 (385)
                      ..+  | +...+.            .+...+.+.|++++|+..+                .+..+...+...|++++|..
T Consensus       214 a~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          214 CLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhhCccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            865  3 222222            2366688899999998888                35567888999999999999


Q ss_pred             HHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHHHHHh
Q 040338          307 YFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLGACCS  361 (385)
Q Consensus       307 ~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~~~~~  361 (385)
                      .+++..+..+  ...+..+...+.+.|++++|.+.|++..+. |+ ...+..+..+...
T Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~  352 (359)
T 3ieg_A          294 ICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQRL  352 (359)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Confidence            9999998777  888899999999999999999999998874 55 4455555555443

>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=99.77  E-value=3.7e-17  Score=146.05  Aligned_cols=303  Identities=11%  Similarity=-0.051  Sum_probs=204.5

Q ss_pred             CCChHHHHHHHHHHHHcccchhhHHhhhhhHHH-HHhhhC--CC-----ChhhHHHHHHHHHhhhccCChHHHHHHHHHH
Q 040338            7 LKSLPIARKIHAQLISTCLISSIFLQLIDDDYR-VFCDIG--PR-----YLFTYNTMINGGVRCLCVGNIKMALHLHGLV   78 (385)
Q Consensus         7 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~A~~-~~~~~~--~~-----~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m   78 (385)
                      .+.+..+...++.+.+.+.....+..++++|.. .|++..  .|     +...+..+...+..   .|++++|...++.+
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~---~g~~~~A~~~~~~a   90 (368)
T 1fch_A           14 VDFWDKLQAELEEMAKRDAEAHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQ---EGDLPNAVLLFEAA   90 (368)
T ss_dssp             --------------------------------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHH---TTCHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHcCCchhhHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHH---CCCHHHHHHHHHHH
Confidence            345666666777776665554445558899988 887543  11     24557777777666   89999999999999


Q ss_pred             HHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchH
Q 040338           79 KKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFE  158 (385)
Q Consensus        79 ~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~  158 (385)
                      .+.. +.+..++..+..+|.+.|++++|.+.|+++.+.+                   +.+..++..+...+...|++++
T Consensus        91 l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------------------~~~~~~~~~l~~~~~~~g~~~~  150 (368)
T 1fch_A           91 VQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-------------------PDNQTALMALAVSFTNESLQRQ  150 (368)
T ss_dssp             HHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-------------------CCCHHHHHHHHHHHHHcCCHHH
Confidence            9874 4477889999999999999999999998876554                   4577889999999999999999


Q ss_pred             HHHHHHHHHHCCCCCCHhhHHH---------------HHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          159 TLCTFIELWNHGFGLSSMLYAT---------------AFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       159 a~~~~~~m~~~g~~p~~~t~~~---------------ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      |...|+++.+.... +...+..               .+..+...|++++|...++.+.+..+..               
T Consensus       151 A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~---------------  214 (368)
T 1fch_A          151 ACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTS---------------  214 (368)
T ss_dssp             HHHHHHHHHHTSTT-TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTS---------------
T ss_pred             HHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCc---------------
Confidence            99999999886322 2222211               2333337889999999999988875421               


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCC
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGP  300 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~  300 (385)
                            ++..++..+...+.+.|++++|+..|++..+  | +..++.                      .+...+...|+
T Consensus       215 ------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~----------------------~l~~~~~~~g~  266 (368)
T 1fch_A          215 ------IDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWN----------------------KLGATLANGNQ  266 (368)
T ss_dssp             ------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH----------------------HHHHHHHHTTC
T ss_pred             ------ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHH----------------------HHHHHHHHcCC
Confidence                  1234556777778888899999999988765  2 233444                      44455555666


Q ss_pred             hhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC------------cchHHHHHHHHHhcCCh
Q 040338          301 VTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT------------CVIWGALLGACCSHYNT  365 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~------------~~~~~~li~~~~~~g~~  365 (385)
                      +++|...++++.+..+  ...+..+...|.+.|++++|.+.|+++... |+            ..+|..+..+|...|++
T Consensus       267 ~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  346 (368)
T 1fch_A          267 SEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQS  346 (368)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCG
T ss_pred             HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCCh
Confidence            7777788888777666  778888999999999999999999887652 22            46899999999999999


Q ss_pred             HHHHHHHHHHH
Q 040338          366 KLAELVMRNLL  376 (385)
Q Consensus       366 ~~a~~~~~~~~  376 (385)
                      ++|..++++..
T Consensus       347 ~~A~~~~~~~l  357 (368)
T 1fch_A          347 DAYGAADARDL  357 (368)
T ss_dssp             GGHHHHHTTCH
T ss_pred             HhHHHhHHHHH
Confidence            99998877543

>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=99.75  E-value=2.1e-18  Score=152.95  Aligned_cols=269  Identities=12%  Similarity=-0.002  Sum_probs=130.7

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLR  112 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  112 (385)
                      ++++|..++++++.|+  +|..+..++..   .|++++|++.|.+      .+|..+|..++..+...|++++|++.++.
T Consensus        18 ~ld~A~~fae~~~~~~--vWs~La~A~l~---~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           18 NLDRAYEFAERCNEPA--VWSQLAKAQLQ---KGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CHHHHHHHHHhCCChH--HHHHHHHHHHH---cCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            6899999999987664  89999999777   8999999999964      35778999999999999999999997765


Q ss_pred             ccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCcc
Q 040338          113 MLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLE  192 (385)
Q Consensus       113 m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~  192 (385)
                      ..+ .                   .+++.+.+.|+.+|.+.|+++++.++++       .|+..+|..+...|...|.++
T Consensus        87 ark-~-------------------~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~ye  139 (449)
T 1b89_A           87 ARK-K-------------------ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYD  139 (449)
T ss_dssp             ------------------------------------------CHHHHTTTTT-------CC----------------CTT
T ss_pred             HHH-h-------------------CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHH
Confidence            544 2                   2557788899999999999999888884       477789999999999999999


Q ss_pred             chhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHH
Q 040338          193 WGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISA  272 (385)
Q Consensus       193 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~  272 (385)
                      +|...|..+                               ..|..++.++.+.|++++|.+.+.++  .++.+|..++.+
T Consensus       140 eA~~~Y~~a-------------------------------~n~~~LA~~L~~Lg~yq~AVea~~KA--~~~~~Wk~v~~a  186 (449)
T 1b89_A          140 AAKLLYNNV-------------------------------SNFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEVCFA  186 (449)
T ss_dssp             THHHHHHHT-------------------------------TCHHHHHHHHHTTTCHHHHHHHHHHH--TCHHHHHHHHHH
T ss_pred             HHHHHHHHh-------------------------------hhHHHHHHHHHHhccHHHHHHHHHHc--CCchhHHHHHHH
Confidence            999999976                               13577888888888999999999988  478999999999


Q ss_pred             HHhcCCCCchHHHH--------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHc--cCCHHHHHHHH
Q 040338          273 FSQAGVLEKPRFFF--------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGL--SGLLGEAKKLI  340 (385)
Q Consensus       273 ~~~~g~~~~a~~~~--------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~--~g~~~~A~~~~  340 (385)
                      |+..|+++.|....        -...++..|.+.|.+++|..+++.......  ...|+-|...|++  -+++.+.+++|
T Consensus       187 Cv~~~ef~lA~~~~l~L~~~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le~ah~~~ftel~il~~ky~p~k~~ehl~~~  266 (449)
T 1b89_A          187 CVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELF  266 (449)
T ss_dssp             HHHTTCHHHHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHcCcHHHHHHHHHHHHhCHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            99999998886655        444688889999999999999999887766  7777777777776  45677777777


Q ss_pred             HhCCCC-------CCcchHHHHHHHHHhcCChHHHHHHH
Q 040338          341 DEMPSK-------PTCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       341 ~~m~~~-------p~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      ..-..-       -+...|..++-.|...++++.|...+
T Consensus       267 ~~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~tm  305 (449)
T 1b89_A          267 WSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITM  305 (449)
T ss_dssp             STTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH
Confidence            654442       24678999999999999999887643

>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=99.75  E-value=1.9e-16  Score=148.84  Aligned_cols=295  Identities=9%  Similarity=-0.054  Sum_probs=222.7

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ..|..+-..+..   .|++++|...|+++.+.. +.+..++..+..+|.+.|++++|++.|+++.+.+            
T Consensus        26 ~~~~~~g~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~------------   89 (537)
T 3fp2_A           26 VQLKNRGNHFFT---AKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK------------   89 (537)
T ss_dssp             HHHHHHHHHHHH---TTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHH---hccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC------------
Confidence            345555556555   899999999999999875 4578899999999999999999999999987655            


Q ss_pred             HHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCC------------------------------------CCC
Q 040338          130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHG------------------------------------FGL  173 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g------------------------------------~~p  173 (385)
                             +.+..++..+..++...|++++|...|+.+....                                    ..|
T Consensus        90 -------p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~  162 (537)
T 3fp2_A           90 -------PDHSKALLRRASANESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLP  162 (537)
T ss_dssp             -------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCC
T ss_pred             -------CchHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccc
Confidence                   3566778888888888888888888886331110                                    011


Q ss_pred             CHhhH------------------------------HHHHHHhcCc--------cCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          174 SSMLY------------------------------ATAFSARASV--------YDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       174 ~~~t~------------------------------~~ll~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                      +....                              ..+...+...        |++++|..+++.+.+..+. +...+..
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~-~~~~~~~  241 (537)
T 3fp2_A          163 SNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTV-DDPLREN  241 (537)
T ss_dssp             CHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHH
T ss_pred             hHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCC-cchhhHH
Confidence            11111                              1111111111        2455555566555544321 1222222


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHH-------
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFF-------  286 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~-------  286 (385)
                      +               ..++..+...+...|++++|...|+...+  |+...+..+...+...|++++|+..+       
T Consensus       242 ~---------------~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  306 (537)
T 3fp2_A          242 A---------------ALALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN  306 (537)
T ss_dssp             H---------------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC
T ss_pred             H---------------HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC
Confidence            2               23456677888899999999999999875  67788888999999999999999998       


Q ss_pred             -----HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHH
Q 040338          287 -----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLG  357 (385)
Q Consensus       287 -----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~  357 (385)
                           ++..+...+...|++++|...++++.+..+  ...+..+...+...|++++|.+.++++.+. | +...|..+..
T Consensus       307 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~  386 (537)
T 3fp2_A          307 PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAE  386 (537)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHH
Confidence                 888999999999999999999999998877  788889999999999999999999988763 4 4668999999


Q ss_pred             HHHhcCChHHHHHHHHHHHhccccCC
Q 040338          358 ACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       358 ~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .|...|++++|...++++.+..+.+.
T Consensus       387 ~~~~~g~~~~A~~~~~~a~~~~~~~~  412 (537)
T 3fp2_A          387 ILTDRGDFDTAIKQYDIAKRLEEVQE  412 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHhCCHHHHHHHHHHHHHcCCcch
Confidence            99999999999999999998776544

>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=99.73  E-value=2.7e-17  Score=146.92  Aligned_cols=268  Identities=10%  Similarity=-0.053  Sum_probs=193.1

Q ss_pred             cCChHHHHH-HHHHHHHhcc---CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCc
Q 040338           65 VGNIKMALH-LHGLVKKFYF---VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDL  140 (385)
Q Consensus        65 ~~~~~~a~~-~~~~m~~~g~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~  140 (385)
                      .|++++|.. .+++..+...   ..+...+..+...+.+.|++++|...|+++.+.+                   +.+.
T Consensus        38 ~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~   98 (368)
T 1fch_A           38 LSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-------------------PKHM   98 (368)
T ss_dssp             --------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-------------------TTCH
T ss_pred             HHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------------------CCCH
Confidence            578888887 7775554321   1135678889999999999999999999987665                   4677


Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      .+|..+..++.+.|++++|...|+++.+.. +.+..++..+...+...|++++|...++.+.+..+..... +..+....
T Consensus        99 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~-~~~~~~~~  176 (368)
T 1fch_A           99 EAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHL-VTPAEEGA  176 (368)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGG-CC------
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHH-HHHHHHHh
Confidence            889999999999999999999999998863 3367889999999999999999999999999875432211 10000000


Q ss_pred             HhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CC---hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHh
Q 040338          221 LKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RN---MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGC  295 (385)
Q Consensus       221 ~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~---~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~  295 (385)
                         +.  ..+ ...+..+ ..+...|++++|...|+++.+  |+   ..++.                      .+...+
T Consensus       177 ---~~--~~~-~~~~~~~-~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~----------------------~l~~~~  227 (368)
T 1fch_A          177 ---GG--AGL-GPSKRIL-GSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQC----------------------GLGVLF  227 (368)
T ss_dssp             ---------------CTT-HHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHH----------------------HHHHHH
T ss_pred             ---hh--hcc-cHHHHHH-HHHhhcccHHHHHHHHHHHHHhCcCcccHHHHH----------------------HHHHHH
Confidence               00  000 0011122 233377899999999998875  22   33333                      444555


Q ss_pred             cccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELV  371 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~  371 (385)
                      ...|++++|...++++.+..+  ...+..+...+.+.|++++|.+.|+++... | +...|..+...|.+.|++++|...
T Consensus       228 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  307 (368)
T 1fch_A          228 NLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEH  307 (368)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence            556667777888888777666  778899999999999999999999998652 4 567899999999999999999999


Q ss_pred             HHHHHhccccC
Q 040338          372 MRNLLQLDVKV  382 (385)
Q Consensus       372 ~~~~~~~~~~~  382 (385)
                      ++++.+..|..
T Consensus       308 ~~~al~~~~~~  318 (368)
T 1fch_A          308 FLEALNMQRKS  318 (368)
T ss_dssp             HHHHHHHHHTC
T ss_pred             HHHHHHhCCCC
Confidence            99999887765

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.72  E-value=7.7e-17  Score=143.99  Aligned_cols=256  Identities=9%  Similarity=-0.048  Sum_probs=189.7

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +...+..+...+.+.|++++|.+.|+++.+.+                   +.+..+|..+...+.+.|++++|+..|++
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  124 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-------------------PGDAEAWQFLGITQAENENEQAAIVALQR  124 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------------------cCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            44557777777777888888888887765544                   34566777788888888888888888888


Q ss_pred             HHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcC
Q 040338          166 LWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEG  245 (385)
Q Consensus       166 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~  245 (385)
                      +.+.. +.+..++..+..++...|++++|...++.+.+..+... ..+..+            ......+..+...+...
T Consensus       125 al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~-~~~~~~------------~~~~~~~~~l~~~~~~~  190 (365)
T 4eqf_A          125 CLELQ-PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYK-YLVKNK------------KGSPGLTRRMSKSPVDS  190 (365)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHH-CC-------------------------------CC
T ss_pred             HHhcC-CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccch-HHHhhh------------ccchHHHHHHHHHHhhh
Confidence            77642 22466777777788888888888888888777542110 001000            01123345667888889


Q ss_pred             CChhHHHHHHHhccc--C---ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHH
Q 040338          246 GSTQKADLAFELMSR--R---NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       246 g~~~~A~~~~~~m~~--~---~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      |++++|+..|+++.+  |   +..++..+...|...|++++|+..+            +|..+..+|...|++++|...+
T Consensus       191 g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  270 (365)
T 4eqf_A          191 SVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAY  270 (365)
T ss_dssp             HHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            999999999999875  3   5778999999999999999999998            8999999999999999999999


Q ss_pred             HHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-------------CcchHHHHHHHHHhcCChHHHHHHH
Q 040338          309 TAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-------------TCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       309 ~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-------------~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      +++.+..+  ...+..+..+|.+.|++++|.+.|+++.+. |             +...|..+..++...|+.+.+....
T Consensus       271 ~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  350 (365)
T 4eqf_A          271 TRALEIQPGFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAAN  350 (365)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            99998877  788889999999999999999999988652 2             2678999999999999999888876


Q ss_pred             HH
Q 040338          373 RN  374 (385)
Q Consensus       373 ~~  374 (385)
                      ++
T Consensus       351 ~~  352 (365)
T 4eqf_A          351 LG  352 (365)
T ss_dssp             TT
T ss_pred             Hh
Confidence            65

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.71  E-value=7.1e-16  Score=137.70  Aligned_cols=251  Identities=11%  Similarity=-0.018  Sum_probs=201.5

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      +...|..+...+..   .|++++|...|+.+.+.. +.+..++..+..+|.+.|++++|...|++..+.+          
T Consensus        64 ~~~~~~~~~~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----------  129 (365)
T 4eqf_A           64 DWPGAFEEGLKRLK---EGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ----------  129 (365)
T ss_dssp             TCTTHHHHHHHHHH---HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             chhHHHHHHHHHHH---CCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----------
Confidence            34557777777666   899999999999999875 4478899999999999999999999999886654          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-----------HhhHHHHHHHhcCccCccchhh
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS-----------SMLYATAFSARASVYDLEWGPH  196 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-----------~~t~~~ll~~~~~~~~~~~a~~  196 (385)
                               +.+..+|..+...|...|++++|...|+++.+.  .|+           ...+..+...+.+.|++++|.+
T Consensus       130 ---------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  198 (365)
T 4eqf_A          130 ---------PNNLKALMALAVSYTNTSHQQDACEALKNWIKQ--NPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKE  198 (365)
T ss_dssp             ---------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CHHHHCC-------------------CCHHHHHHHH
T ss_pred             ---------CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHH
Confidence                     356789999999999999999999999999874  332           2223345788999999999999


Q ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHH
Q 040338          197 LHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAF  273 (385)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~  273 (385)
                      .++++.+..+..                     ++..++..+...|...|++++|+..|++..+   .+..+|..+..+|
T Consensus       199 ~~~~al~~~p~~---------------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~  257 (365)
T 4eqf_A          199 LYLEAAHQNGDM---------------------IDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATL  257 (365)
T ss_dssp             HHHHHHHHSCSS---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHhCcCc---------------------cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            999999875431                     1334456677777778899999999998865   3577899999999


Q ss_pred             HhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------------hhhHHHHHHHH
Q 040338          274 SQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------------TCYFVCMVDLL  327 (385)
Q Consensus       274 ~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------------~~~~~~li~~~  327 (385)
                      ...|++++|+..+            ++..+..+|...|++++|...++++.+..+              ...+..+..++
T Consensus       258 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  337 (365)
T 4eqf_A          258 ANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIAL  337 (365)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHH
Confidence            9999999999888            788899999999999999999999887664              46788899999


Q ss_pred             HccCCHHHHHHHHHhCC
Q 040338          328 GLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       328 ~~~g~~~~A~~~~~~m~  344 (385)
                      ...|+.+.+.++.++-.
T Consensus       338 ~~~g~~~~a~~~~~~~l  354 (365)
T 4eqf_A          338 SLMDQPELFQAANLGDL  354 (365)
T ss_dssp             HHHTCHHHHHHHHTTCC
T ss_pred             HHcCcHHHHHHHHHhhH
Confidence            99999999999887643

>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=99.69  E-value=3.4e-16  Score=138.88  Aligned_cols=251  Identities=8%  Similarity=0.006  Sum_probs=112.6

Q ss_pred             cCCChHHHHHHHHHHHHcccchhhHHh---------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHH
Q 040338            6 SLKSLPIARKIHAQLISTCLISSIFLQ---------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHG   76 (385)
Q Consensus         6 ~~~~~~~a~~~~~~~~~~~~~~~~~~~---------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~   76 (385)
                      +.|+++.|.+.++++..    |+++..         ++++|.+.|.+  .+|..+|..++.++..   .|++++|..+++
T Consensus        15 ~~~~ld~A~~fae~~~~----~~vWs~La~A~l~~g~~~eAIdsfik--a~D~~~y~~V~~~ae~---~g~~EeAi~yl~   85 (449)
T 1b89_A           15 HIGNLDRAYEFAERCNE----PAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANT---SGNWEELVKYLQ   85 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCCC----hHHHHHHHHHHHHcCCHHHHHHHHHc--CCCHHHHHHHHHHHHh---CCCHHHHHHHHH
Confidence            56889999999999944    334333         99999999976  4677799999998655   899999999888


Q ss_pred             HHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCc
Q 040338           77 LVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFG  156 (385)
Q Consensus        77 ~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~  156 (385)
                      ...+.  .+++.+.+.++.+|++.|+++++.++++                         .|+..+|+.+...|...|++
T Consensus        86 ~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------------------------~pn~~a~~~IGd~~~~~g~y  138 (449)
T 1b89_A           86 MARKK--ARESYVETELIFALAKTNRLAELEEFIN-------------------------GPNNAHIQQVGDRCYDEKMY  138 (449)
T ss_dssp             -------------------------CHHHHTTTTT-------------------------CC----------------CT
T ss_pred             HHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------------------------CCcHHHHHHHHHHHHHcCCH
Confidence            77764  4568889999999999999999988874                         36666888888888888888


Q ss_pred             hHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC--------C
Q 040338          157 FETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG--------I  228 (385)
Q Consensus       157 ~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~--------~  228 (385)
                      ++|..+|..+         ..|..+..++.+.|++++|.+.+..+      .++.+|..++.+|...|+++        +
T Consensus       139 eeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L  203 (449)
T 1b89_A          139 DAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI  203 (449)
T ss_dssp             TTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTT
T ss_pred             HHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHH
Confidence            8888888866         47888888888888888888888877      36788888888888887555        2


Q ss_pred             CchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhc--CCCCchHHHH-----------------
Q 040338          229 ESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQA--GVLEKPRFFF-----------------  286 (385)
Q Consensus       229 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~--g~~~~a~~~~-----------------  286 (385)
                      .....-...++..|.+.|++++|..+++....   ..+..|+.|.-.|++-  ++..+.++.|                 
T Consensus       204 ~~~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~  283 (449)
T 1b89_A          204 VVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAH  283 (449)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTT
T ss_pred             HhCHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            22223345688999999999999999987765   3566777777777654  4556666666                 


Q ss_pred             HHHHHHHHhcccCChhhHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHY  307 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~  307 (385)
                      .|..+.-.|.+.++++.|...
T Consensus       284 ~w~e~~~ly~~~~e~d~A~~t  304 (449)
T 1b89_A          284 LWAELVFLYDKYEEYDNAIIT  304 (449)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhhchHHHHHHH
Confidence            677777777888888877653

>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=99.69  E-value=2.1e-15  Score=132.04  Aligned_cols=259  Identities=11%  Similarity=-0.023  Sum_probs=199.9

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ..|..+...+..   .|++++|..+++.+.+.. +.+...+..+..++.+.|++++|.+.|+++.+.+            
T Consensus        22 ~~~~~~a~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~------------   85 (327)
T 3cv0_A           22 ENPMEEGLSMLK---LANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD------------   85 (327)
T ss_dssp             SCHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHH---hccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC------------
Confidence            445555666555   899999999999999875 3477888999999999999999999999886554            


Q ss_pred             HHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC-HhhHHHH--------------HH-HhcCccCccc
Q 040338          130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS-SMLYATA--------------FS-ARASVYDLEW  193 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~l--------------l~-~~~~~~~~~~  193 (385)
                             +.+..++..+...+...|++++|...++++.+.  .|+ ...+..+              .. .+...|++++
T Consensus        86 -------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (327)
T 3cv0_A           86 -------PKDIAVHAALAVSHTNEHNANAALASLRAWLLS--QPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRE  156 (327)
T ss_dssp             -------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--STTTTTC--------------------CCTTSHHHHHH
T ss_pred             -------cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHH
Confidence                   456788999999999999999999999999875  333 2333333              22 4788899999


Q ss_pred             hhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHH
Q 040338          194 GPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLI  270 (385)
Q Consensus       194 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li  270 (385)
                      |.+.++.+.+....                       +..++..+...+.+.|++++|...+++..+  | +..++    
T Consensus       157 A~~~~~~~~~~~~~-----------------------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~----  209 (327)
T 3cv0_A          157 CRTLLHAALEMNPN-----------------------DAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLW----  209 (327)
T ss_dssp             HHHHHHHHHHHSTT-----------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH----
T ss_pred             HHHHHHHHHhhCCC-----------------------CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHH----
Confidence            99999999887532                       334556777788888899999999998865  2 23333    


Q ss_pred             HHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C
Q 040338          271 SAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P  347 (385)
Q Consensus       271 ~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p  347 (385)
                                        ..+...+...|++++|...++++.+..+  ...+..+...|.+.|++++|.+.|++.... |
T Consensus       210 ------------------~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~  271 (327)
T 3cv0_A          210 ------------------NKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQV  271 (327)
T ss_dssp             ------------------HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHT
T ss_pred             ------------------HHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC
Confidence                              3444555556667777788888777666  777888999999999999999999887653 4


Q ss_pred             C-------------cchHHHHHHHHHhcCChHHHHHHHHHHHhc
Q 040338          348 T-------------CVIWGALLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       348 ~-------------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                      +             ...|..+..+|...|++++|..++++..+.
T Consensus       272 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  315 (327)
T 3cv0_A          272 GGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEP  315 (327)
T ss_dssp             TSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSHH
T ss_pred             ccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            3             668889999999999999999998876543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.69  E-value=1.2e-15  Score=131.74  Aligned_cols=241  Identities=10%  Similarity=-0.084  Sum_probs=174.4

Q ss_pred             HhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhh
Q 040338           98 VKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSML  177 (385)
Q Consensus        98 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t  177 (385)
                      ...|++..|+..+++....++                  .+.....-.+..+|...|++++|+..++.    .-+|+..+
T Consensus        10 ~~~g~y~~ai~~~~~~~~~~p------------------~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a   67 (291)
T 3mkr_A           10 FYIGSYQQCINEAQRVKPSSP------------------ERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQA   67 (291)
T ss_dssp             HHTTCHHHHHHHHHHSCCCSH------------------HHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCCc------------------hhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHH
Confidence            346777777777766544332                  11123445567788888888888876644    13556777


Q ss_pred             HHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHh
Q 040338          178 YATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFEL  257 (385)
Q Consensus       178 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  257 (385)
                      +..+...+...++.++|++.++++...+..|+...                     .+..+...+...|++++|+..+++
T Consensus        68 ~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~---------------------~~~~la~~~~~~g~~~~Al~~l~~  126 (291)
T 3mkr_A           68 VRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTT---------------------FLLMAASIYFYDQNPDAALRTLHQ  126 (291)
T ss_dssp             HHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHH---------------------HHHHHHHHHHHTTCHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHH---------------------HHHHHHHHHHHCCCHHHHHHHHhC
Confidence            77788888888888888888888877664443322                     234445566666777777777776


Q ss_pred             cccCChhhHHHHHHHHHhcCCCCchHHHH----------HHHHHH----HHhcccCChhhHHHHHHHHHhccc--hhhHH
Q 040338          258 MSRRNMISWMVLISAFSQAGVLEKPRFFF----------FFVSLL----SGCSHSGPVTKGKHYFTAMAKFTY--TCYFV  321 (385)
Q Consensus       258 m~~~~~~~~~~li~~~~~~g~~~~a~~~~----------~~~~l~----~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~  321 (385)
                        ..+...+..++..|.+.|++++|++.+          +...+.    ..+...|++++|..+|+++.+..+  ...++
T Consensus       127 --~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~  204 (291)
T 3mkr_A          127 --GDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLN  204 (291)
T ss_dssp             --CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHH
T ss_pred             --CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHH
Confidence              345667777777777777777777776          222222    333456899999999999998877  88889


Q ss_pred             HHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHH-HHHHHHHHHhccccCC
Q 040338          322 CMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKL-AELVMRNLLQLDVKVF  383 (385)
Q Consensus       322 ~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~~~~~~  383 (385)
                      .+..++.+.|++++|...|++.... | +..++..++..+...|+.++ +.++++++++.+|..+
T Consensus       205 ~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P~~~  269 (291)
T 3mkr_A          205 GQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHRSHP  269 (291)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCh
Confidence            9999999999999999999997763 4 56789999999999999976 6789999999888754

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.66  E-value=3.1e-13  Score=125.58  Aligned_cols=318  Identities=9%  Similarity=-0.113  Sum_probs=204.2

Q ss_pred             hhhhHHHHHhhhC-CCChhhHHHHHHHHHh-hhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh----cCChhHH
Q 040338           33 LIDDDYRVFCDIG-PRYLFTYNTMINGGVR-CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK----CGAVDYA  106 (385)
Q Consensus        33 ~~~~A~~~~~~~~-~~~~~~~~~li~~~~~-~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~g~~~~a  106 (385)
                      ++++|...|++.. ..++..+..|-..+.. .+-.+++++|.+.|++..+.|   +...+..|...|..    .++.++|
T Consensus        58 ~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A  134 (490)
T 2xm6_A           58 DLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAES  134 (490)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            5666666665443 2233344433333221 001456666666666666543   44555556666665    5666666


Q ss_pred             HHHHHhccCCCccc--------------cccchHHHHHHhcCCC-CCCcchHHHHHHHHHh----CCCchHHHHHHHHHH
Q 040338          107 ESAFLRMLNPSLFC--------------WKFGIIRLLIMFQKMP-ERDLVSWNTMISILTR----HGFGFETLCTFIELW  167 (385)
Q Consensus       107 ~~~~~~m~~~~~~~--------------~~~~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~  167 (385)
                      .+.|++..+.+...              ..++.++|.+.|.+.. ..+...+..|...|..    .+++++|+.+|++..
T Consensus       135 ~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~  214 (490)
T 2xm6_A          135 VKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSA  214 (490)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHH
Confidence            66666654432100              0022222222222211 1234445555555554    555666666666555


Q ss_pred             HCCCCCCHhhHHHHHHHhcC----ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHH
Q 040338          168 NHGFGLSSMLYATAFSARAS----VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA  243 (385)
Q Consensus       168 ~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~  243 (385)
                      +.|   +...+..+...+..    .++.++|...++...+.|                         +...+..+...|.
T Consensus       215 ~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~-------------------------~~~a~~~lg~~y~  266 (490)
T 2xm6_A          215 TSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG-------------------------NSIAQFRLGYILE  266 (490)
T ss_dssp             HTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT-------------------------CHHHHHHHHHHHH
T ss_pred             HCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-------------------------CHHHHHHHHHHHH
Confidence            543   23333344444432    455555665555555443                         2334455556666


Q ss_pred             c----CCChhHHHHHHHhcccC-ChhhHHHHHHHHHhc-----CCCCchHHHH----------HHHHHHHHhcccC---C
Q 040338          244 E----GGSTQKADLAFELMSRR-NMISWMVLISAFSQA-----GVLEKPRFFF----------FFVSLLSGCSHSG---P  300 (385)
Q Consensus       244 ~----~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~-----g~~~~a~~~~----------~~~~l~~~~~~~~---~  300 (385)
                      .    .++.++|+..|++..+. +...+..+...|...     +++++|+..+          .+..+...|...|   +
T Consensus       267 ~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~~g~~~~  346 (490)
T 2xm6_A          267 QGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQGDATAQANLGAIYFRLGSEEE  346 (490)
T ss_dssp             HTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCCHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCccc
Confidence            6    78999999999988764 667778888888877     8888999888          6666777776655   8


Q ss_pred             hhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCCCCcchHHHHHHHHHh----cCChHHHHHHH
Q 040338          301 VTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSKPTCVIWGALLGACCS----HYNTKLAELVM  372 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~----~g~~~~a~~~~  372 (385)
                      .++|.+.|++..+.+.+..+..+...|..    .+++++|.+.|++..+..+...+..|...|..    .++.++|...|
T Consensus       347 ~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~  426 (490)
T 2xm6_A          347 HKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQGLSAAQVQLGEIYYYGLGVERDYVQAWAWF  426 (490)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            89999999999998888888889999988    89999999999998877678888899999998    89999999999


Q ss_pred             HHHHhcccc
Q 040338          373 RNLLQLDVK  381 (385)
Q Consensus       373 ~~~~~~~~~  381 (385)
                      ++..+.+++
T Consensus       427 ~~A~~~~~~  435 (490)
T 2xm6_A          427 DTASTNDMN  435 (490)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHHHCCCC
Confidence            999998843

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.61  E-value=1.6e-14  Score=124.66  Aligned_cols=262  Identities=11%  Similarity=0.007  Sum_probs=155.3

Q ss_pred             hhhhHHHHHhhhCCCCh----hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHH
Q 040338           33 LIDDDYRVFCDIGPRYL----FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAES  108 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~  108 (385)
                      ++++|...++.....++    ...-.+.+++..   .|+++.|+..++.    .-+|+..++..+...+...++.++|++
T Consensus        14 ~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~---~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~~A~~   86 (291)
T 3mkr_A           14 SYQQCINEAQRVKPSSPERDVERDVFLYRAYLA---QRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRDAIVA   86 (291)
T ss_dssp             CHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHH---TTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHHHHHH
T ss_pred             HHHHHHHHHHhcccCCchhhHHHHHHHHHHHHH---CCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHHHHHH
Confidence            66666666665443221    122344555555   6777776654433    124455666666667777777777777


Q ss_pred             HHHhccCCCccccccchHHHHHHhcCCCCC-CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC
Q 040338          109 AFLRMLNPSLFCWKFGIIRLLIMFQKMPER-DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS  187 (385)
Q Consensus       109 ~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  187 (385)
                      .++++...+.                  .| +...+..+...+.+.|++++|++.+++      +.+...+..+...+.+
T Consensus        87 ~l~~ll~~~~------------------~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~  142 (291)
T 3mkr_A           87 ELDREMSRSV------------------DVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLK  142 (291)
T ss_dssp             HHHHHHHSCC------------------CCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHH
T ss_pred             HHHHHHhccc------------------CCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHH
Confidence            7766644332                  23 344455555666777777777777665      3455666666667777


Q ss_pred             ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-Chh
Q 040338          188 VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMI  264 (385)
Q Consensus       188 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~  264 (385)
                      .|++++|.+.++.+.+..  |+....                   ......+..+...|++++|..+|+++.+  | +..
T Consensus       143 ~g~~~~A~~~l~~~~~~~--p~~~~~-------------------~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~  201 (291)
T 3mkr_A          143 LDRLDLARKELKKMQDQD--EDATLT-------------------QLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLL  201 (291)
T ss_dssp             TTCHHHHHHHHHHHHHHC--TTCHHH-------------------HHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHH
T ss_pred             CCCHHHHHHHHHHHHhhC--cCcHHH-------------------HHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHH
Confidence            777777777777776654  221100                   0112233334445667777777776654  2 333


Q ss_pred             hHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHH-HHHHHH
Q 040338          265 SWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGE-AKKLID  341 (385)
Q Consensus       265 ~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~-A~~~~~  341 (385)
                      .                      ++.+..++.+.|++++|...++++.+..+  +.++..++..+...|+.++ +.++++
T Consensus       202 ~----------------------~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~  259 (291)
T 3mkr_A          202 L----------------------LNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLS  259 (291)
T ss_dssp             H----------------------HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             H----------------------HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            3                      44445555566667777888888887777  7788888888888998876 567887


Q ss_pred             hCCC-CCCcchHHHHHHHHHhcCChHHHHHH
Q 040338          342 EMPS-KPTCVIWGALLGACCSHYNTKLAELV  371 (385)
Q Consensus       342 ~m~~-~p~~~~~~~li~~~~~~g~~~~a~~~  371 (385)
                      ++.+ .|+...   +.....+.+.++++..-
T Consensus       260 ~~~~~~P~~~~---~~d~~~~~~~fd~~~~~  287 (291)
T 3mkr_A          260 QLKDAHRSHPF---IKEYRAKENDFDRLVLQ  287 (291)
T ss_dssp             HHHHHCTTCHH---HHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCChH---HHHHHHHHHHHHHHHHH
Confidence            7765 355432   33344555555555443

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.58  E-value=2.9e-12  Score=120.24  Aligned_cols=351  Identities=10%  Similarity=0.041  Sum_probs=225.6

Q ss_pred             cCCChHHHHHHHHHHHHcccc-hhhHHh---------hhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHHHH
Q 040338            6 SLKSLPIARKIHAQLISTCLI-SSIFLQ---------LIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMALH   73 (385)
Q Consensus         6 ~~~~~~~a~~~~~~~~~~~~~-~~~~~~---------~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a~~   73 (385)
                      +.|+++.|+.+++++++.... +..+..         ++++|..+|++..  .|++..|...+.-...  ..|+++.|.+
T Consensus        24 ~~~~~~~a~~~~e~al~~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~~~~~~--~~~~~~~a~~  101 (530)
T 2ooe_A           24 QNQPIDKARKTYERLVAQFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRE--TKGKLPSYKE  101 (530)
T ss_dssp             HSSCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHHHHHHH--HTTTSTTHHH
T ss_pred             HhCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHHHHHHH--HccchhhHHH
Confidence            468899999999999886432 223332         8889999999876  4666666666643221  1466666554


Q ss_pred             ----HHHHHHHh-ccCC-CchHHHhHHHHHHh---------cCChhHHHHHHHhccCCCcc----ccc------------
Q 040338           74 ----LHGLVKKF-YFVS-DESIAKSSIDMHVK---------CGAVDYAESAFLRMLNPSLF----CWK------------  122 (385)
Q Consensus        74 ----~~~~m~~~-g~~~-~~~~~~~li~~~~~---------~g~~~~a~~~~~~m~~~~~~----~~~------------  122 (385)
                          +|+...+. |..| +...|...+....+         .|+++.|.++|++..+....    .|.            
T Consensus       102 ~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~~~~~~~e~~~~~~  181 (530)
T 2ooe_A          102 KMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIH  181 (530)
T ss_dssp             HHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHHHHHHHHHHHHCHH
T ss_pred             HHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHhhchh
Confidence                77766654 5444 45677777776654         67888999999887662110    111            


Q ss_pred             ----------cchHHHHHHhc----------CC---CCCC--------cchHHHHHHHHHhC----CCc----hHHHHHH
Q 040338          123 ----------FGIIRLLIMFQ----------KM---PERD--------LVSWNTMISILTRH----GFG----FETLCTF  163 (385)
Q Consensus       123 ----------~~~~~a~~~~~----------~~---~~~~--------~~~~~~li~~~~~~----~~~----~~a~~~~  163 (385)
                                +.+..|..++.          ..   .+|+        ...|...+......    ++.    +++..+|
T Consensus       182 ~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y  261 (530)
T 2ooe_A          182 LAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAY  261 (530)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHH
Confidence                      12222322221          10   0111        12333333222211    111    2445555


Q ss_pred             HHHHHCCCCCCHhhHHHHHHHhcC-------ccCcc-------chhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCC
Q 040338          164 IELWNHGFGLSSMLYATAFSARAS-------VYDLE-------WGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIE  229 (385)
Q Consensus       164 ~~m~~~g~~p~~~t~~~ll~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~  229 (385)
                      ++.... .+-+...|......+.+       .|+++       +|..+++..++.-                      .+
T Consensus       262 ~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~----------------------~p  318 (530)
T 2ooe_A          262 EQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTL----------------------LK  318 (530)
T ss_dssp             HHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTT----------------------CS
T ss_pred             HHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHh----------------------Cc
Confidence            555543 11234444444444432       45554       5555555554311                      12


Q ss_pred             chhhHHHHHHHHHHcCCChhHHHHHHHhccc--CC-h-hhHHHHHHHHHhcCCCCchHHHH------------HHHHHHH
Q 040338          230 SSIQIGKALVTMYAEGGSTQKADLAFELMSR--RN-M-ISWMVLISAFSQAGVLEKPRFFF------------FFVSLLS  293 (385)
Q Consensus       230 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-~-~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~  293 (385)
                      .+...|..++..+.+.|++++|..+|++..+  |+ . ..|...+..+.+.|++++|.++|            .|.....
T Consensus       319 ~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~  398 (530)
T 2ooe_A          319 KNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAAL  398 (530)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHH
Confidence            2355667778888888999999999998875  33 2 47888888888899999999888            2222111


Q ss_pred             H-hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-C----cchHHHHHHHHHhcCC
Q 040338          294 G-CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-T----CVIWGALLGACCSHYN  364 (385)
Q Consensus       294 ~-~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~----~~~~~~li~~~~~~g~  364 (385)
                      . +...|+.++|..+|+...+..+  +..+..++..+.+.|+.++|..+|++.... | +    ...|...+......|+
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            1 2358999999999999988777  888999999999999999999999998653 2 2    2378888998999999


Q ss_pred             hHHHHHHHHHHHhcccc
Q 040338          365 TKLAELVMRNLLQLDVK  381 (385)
Q Consensus       365 ~~~a~~~~~~~~~~~~~  381 (385)
                      .+.+..+.+++.+.-|.
T Consensus       479 ~~~~~~~~~r~~~~~p~  495 (530)
T 2ooe_A          479 LASILKVEKRRFTAFRE  495 (530)
T ss_dssp             HHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHCch
Confidence            99999999999887664

>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=99.58  E-value=1.6e-12  Score=128.69  Aligned_cols=313  Identities=10%  Similarity=0.031  Sum_probs=227.1

Q ss_pred             hhhhHHHHHhhhC-CCC-----hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHH
Q 040338           33 LIDDDYRVFCDIG-PRY-----LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYA  106 (385)
Q Consensus        33 ~~~~A~~~~~~~~-~~~-----~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a  106 (385)
                      .+.+|..+++++. .|+     ...-+.++.+..+    -+..+..++.......    +   ...+...+...|.+++|
T Consensus      1000 lp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIk----aD~~Rv~eyI~kLd~~----d---~~eIA~Iai~lglyEEA 1068 (1630)
T 1xi4_A         1000 LPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIK----ADRTRVMEYINRLDNY----D---APDIANIAISNELFEEA 1068 (1630)
T ss_pred             CHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHH----hChhhHHHHHHHhhhc----c---HHHHHHHHHhCCCHHHH
Confidence            5566666666554 221     2334445544444    1334444443333311    1   23355667778899999


Q ss_pred             HHHHHhccCCCc----cc-cccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHH
Q 040338          107 ESAFLRMLNPSL----FC-WKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATA  181 (385)
Q Consensus       107 ~~~~~~m~~~~~----~~-~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~l  181 (385)
                      ..+|++....+.    .. ..+++++|.++..+...  ..+|..+..++...|++++|++.|.+.      -|...|..+
T Consensus      1069 f~IYkKa~~~~~A~~VLie~i~nldrAiE~Aervn~--p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eV 1140 (1630)
T 1xi4_A         1069 FAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERCNE--PAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEV 1140 (1630)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhHHHHHHHHHhcCC--HHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHH
Confidence            999988753221    11 11888888888887744  567899999999999999999999663      467788889


Q ss_pred             HHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC------CCchhhHHHHHHHHHHcCCChhHHHHHH
Q 040338          182 FSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG------IESSIQIGKALVTMYAEGGSTQKADLAF  255 (385)
Q Consensus       182 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~------~~~~~~~~~~li~~~~~~g~~~~A~~~~  255 (385)
                      +.++.+.|++++|.+.+....+..  +++...+.+..+|++.++.+      ..++...|..+...|...|++++|..+|
T Consensus      1141 a~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y 1218 (1630)
T 1xi4_A         1141 VQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLY 1218 (1630)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHHhCCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            999999999999999999887765  44444445888888887666      5566677888999999999999999999


Q ss_pred             HhcccCChhhHHHHHHHHHhcCCCCchHHHH-------HHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHH
Q 040338          256 ELMSRRNMISWMVLISAFSQAGVLEKPRFFF-------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLG  328 (385)
Q Consensus       256 ~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~-------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~  328 (385)
                      ...     ..|..+...|++.|++++|++.+       +|..+-.+|...|++..|......+...  +..+..++..|.
T Consensus      1219 ~kA-----~ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~--~deLeeli~yYe 1291 (1630)
T 1xi4_A         1219 NNV-----SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH--ADELEELINYYQ 1291 (1630)
T ss_pred             Hhh-----hHHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcC--HHHHHHHHHHHH
Confidence            886     48999999999999999999999       8999999999999998888876643222  566778999999


Q ss_pred             ccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhc--CChHHHHHHHH
Q 040338          329 LSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSH--YNTKLAELVMR  373 (385)
Q Consensus       329 ~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~--g~~~~a~~~~~  373 (385)
                      +.|.+++|+.+++.....  .+...|+-|...|++.  ++..++.++|.
T Consensus      1292 ~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~ 1340 (1630)
T 1xi4_A         1292 DRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFW 1340 (1630)
T ss_pred             HcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            999999999999887653  3444666666666653  33444444444

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.58  E-value=2.4e-12  Score=118.88  Aligned_cols=315  Identities=8%  Similarity=-0.090  Sum_probs=200.8

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh-----c--cCC-CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccc
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF-----Y--FVS-DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFC  120 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-----g--~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~  120 (385)
                      ...||.|-..+..   .|+.++|++.|++..+.     +  ..| ...+|+.+..+|...|++++|...+++..+     
T Consensus        51 a~~yn~Lg~~~~~---~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~-----  122 (472)
T 4g1t_A           51 ATMCNLLAYLKHL---KGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKH-----  122 (472)
T ss_dssp             CHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-----
T ss_pred             HHHHHHHHHHHHH---CCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH-----
Confidence            4568887777666   89999999999987653     1  122 356889999999999999999999876532     


Q ss_pred             cccchHHHHHHhcCCC---CC-CcchHHHHHHHHHhC--CCchHHHHHHHHHHHCCCCCC-HhhHHHHHHH---hcCccC
Q 040338          121 WKFGIIRLLIMFQKMP---ER-DLVSWNTMISILTRH--GFGFETLCTFIELWNHGFGLS-SMLYATAFSA---RASVYD  190 (385)
Q Consensus       121 ~~~~~~~a~~~~~~~~---~~-~~~~~~~li~~~~~~--~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~---~~~~~~  190 (385)
                                +.....   .+ ...+++.+..++...  +++++|+..|++..+.  .|+ ...+..+..+   +...++
T Consensus       123 ----------i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~--~p~~~~~~~~~~~~~~~l~~~~~  190 (472)
T 4g1t_A          123 ----------VCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK--KPKNPEFTSGLAIASYRLDNWPP  190 (472)
T ss_dssp             ----------HHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHSCC
T ss_pred             ----------HhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCchH
Confidence                      222211   11 234555555555443  4688899999888774  453 3333333333   345567


Q ss_pred             ccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCC----C------------CCchhhHHHHHHHHHHcCCChhHHHHH
Q 040338          191 LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCN----G------------IESSIQIGKALVTMYAEGGSTQKADLA  254 (385)
Q Consensus       191 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~----~------------~~~~~~~~~~li~~~~~~g~~~~A~~~  254 (385)
                      .++|++.++..++..+ .+..++..+...+...+..    +            .+.+..++..+...|...|++++|...
T Consensus       191 ~~~al~~~~~al~l~p-~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~  269 (472)
T 4g1t_A          191 SQNAIDPLRQAIRLNP-DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIEL  269 (472)
T ss_dssp             CCCTHHHHHHHHHHCS-SCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCC-cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHH
Confidence            7788888888877653 3445555555555554432    2            455667888999999999999999999


Q ss_pred             HHhccc--C-ChhhHHHHHHHHHhc-------------------CCCCchHHHH------------HHHHHHHHhcccCC
Q 040338          255 FELMSR--R-NMISWMVLISAFSQA-------------------GVLEKPRFFF------------FFVSLLSGCSHSGP  300 (385)
Q Consensus       255 ~~~m~~--~-~~~~~~~li~~~~~~-------------------g~~~~a~~~~------------~~~~l~~~~~~~~~  300 (385)
                      +++..+  | +..++..+...|...                   +..++|+..+            ++..+...+...|+
T Consensus       270 ~~~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~  349 (472)
T 4g1t_A          270 LKKALEYIPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQ  349 (472)
T ss_dssp             HHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTC
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhcc
Confidence            998875  4 445666665555322                   1123344444            67788899999999


Q ss_pred             hhhHHHHHHHHHhccc-----hhhHHHHHH-HHHccCCHHHHHHHHHhCCC-------------------------C-CC
Q 040338          301 VTKGKHYFTAMAKFTY-----TCYFVCMVD-LLGLSGLLGEAKKLIDEMPS-------------------------K-PT  348 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~-----~~~~~~li~-~~~~~g~~~~A~~~~~~m~~-------------------------~-p~  348 (385)
                      +++|...|++..+..+     ...+..+.. .+...|+.++|+..|++...                         . .+
T Consensus       350 ~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~  429 (472)
T 4g1t_A          350 YEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGAD  429 (472)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-C
T ss_pred             HHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            9999999999887655     222333332 23467899999988876532                         1 34


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHHHhccccCCC
Q 040338          349 CVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       349 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      ..+|..+...|...|++++|++.|++.++.++..+.
T Consensus       430 ~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~  465 (472)
T 4g1t_A          430 SEALHVLAFLQELNEKMQQADEDSERGLESGSLIPS  465 (472)
T ss_dssp             TTHHHHHHHHHHHHHHCC------------------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCc
Confidence            678999999999999999999999999998887654

>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=99.58  E-value=5.2e-13  Score=116.75  Aligned_cols=244  Identities=9%  Similarity=-0.032  Sum_probs=182.7

Q ss_pred             hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|..+|+++.   +.+...|..+...+..   .|++++|...++.+.+.. +.+..++..+...|...|++++|.+.
T Consensus        36 ~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~  111 (327)
T 3cv0_A           36 NLAEAALAFEAVCQAAPEREEAWRSLGLTQAE---NEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALAS  111 (327)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            6777777777654   3456677777777666   899999999999999874 44778899999999999999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHH--------------HH-HHHhCCCchHHHHHHHHHHHCCCCCC
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTM--------------IS-ILTRHGFGFETLCTFIELWNHGFGLS  174 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l--------------i~-~~~~~~~~~~a~~~~~~m~~~g~~p~  174 (385)
                      ++++.+.+.                   .+...+..+              .. .+...|++++|...++++.+.. +.+
T Consensus       112 ~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~  171 (327)
T 3cv0_A          112 LRAWLLSQP-------------------QYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PND  171 (327)
T ss_dssp             HHHHHHTST-------------------TTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTC
T ss_pred             HHHHHHhCC-------------------ccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCC
Confidence            998865542                   222333332              22 3777899999999999998763 336


Q ss_pred             HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHH
Q 040338          175 SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLA  254 (385)
Q Consensus       175 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  254 (385)
                      ...+..+...+...|++++|.+.++.+.+..+                       .+..++..+...+...|++++|...
T Consensus       172 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-----------------------~~~~~~~~l~~~~~~~~~~~~A~~~  228 (327)
T 3cv0_A          172 AQLHASLGVLYNLSNNYDSAAANLRRAVELRP-----------------------DDAQLWNKLGATLANGNRPQEALDA  228 (327)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-----------------------TCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-----------------------CcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            78888999999999999999999999988743                       2334567778888888999999999


Q ss_pred             HHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--------------h
Q 040338          255 FELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------------T  317 (385)
Q Consensus       255 ~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------------~  317 (385)
                      |++..+  | +..++..+...|...|                      ++++|.+.++++.+..+              .
T Consensus       229 ~~~a~~~~~~~~~~~~~l~~~~~~~g----------------------~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~  286 (327)
T 3cv0_A          229 YNRALDINPGYVRVMYNMAVSYSNMS----------------------QYDLAAKQLVRAIYMQVGGTTPTGEASREATR  286 (327)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTT----------------------CHHHHHHHHHHHHHHHTTSCC-----CCTHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHhc----------------------cHHHHHHHHHHHHHhCCccccccccchhhcCH
Confidence            998865  3 3445555555555554                      55555555555544332              4


Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ..+..+..++.+.|++++|..++++..+
T Consensus       287 ~~~~~l~~~~~~~g~~~~A~~~~~~~l~  314 (327)
T 3cv0_A          287 SMWDFFRMLLNVMNRPDLVELTYAQNVE  314 (327)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHTTCCSH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            5677889999999999999999987654

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.57  E-value=4.1e-12  Score=118.01  Aligned_cols=314  Identities=11%  Similarity=-0.076  Sum_probs=219.7

Q ss_pred             HHHHHhhhC-CCChhhHHHHHHHHHh-hhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh----cCChhHHHHHH
Q 040338           37 DYRVFCDIG-PRYLFTYNTMINGGVR-CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK----CGAVDYAESAF  110 (385)
Q Consensus        37 A~~~~~~~~-~~~~~~~~~li~~~~~-~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~g~~~~a~~~~  110 (385)
                      +...+.... ..++..+..+-..|.. ....+++++|...|+...+.|   +...+..|...|..    .++.++|.+.|
T Consensus        26 ~~~~~~~~a~~g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~  102 (490)
T 2xm6_A           26 NLEQLKQKAESGEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWY  102 (490)
T ss_dssp             CHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            344444333 4466665555555432 112799999999999998864   67788889999998    89999999999


Q ss_pred             HhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHh----CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhc
Q 040338          111 LRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTR----HGFGFETLCTFIELWNHGFGLSSMLYATAFSARA  186 (385)
Q Consensus       111 ~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  186 (385)
                      ++..+.+                     +...+..|-..|..    .+++++|+.+|++..+.|   +...+..+...|.
T Consensus       103 ~~a~~~~---------------------~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~  158 (490)
T 2xm6_A          103 KKAALKG---------------------LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYF  158 (490)
T ss_dssp             HHHHHTT---------------------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH
T ss_pred             HHHHHCC---------------------CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH
Confidence            9986543                     23344445555555    555666666666555543   2333334444443


Q ss_pred             C----ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHh----cCCCC----------CCchhhHHHHHHHHHHc----
Q 040338          187 S----VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLK----CGCNG----------IESSIQIGKALVTMYAE----  244 (385)
Q Consensus       187 ~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~----------~~~~~~~~~~li~~~~~----  244 (385)
                      .    .++.++|.+.|+...+.|   +...+..|-..|..    .++.+          ...+...+..+...|..    
T Consensus       159 ~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~g~  235 (490)
T 2xm6_A          159 EGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSGDELGQLHLADMYYFGIGV  235 (490)
T ss_dssp             HTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSS
T ss_pred             cCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCC
Confidence            3    455555666665555543   33444444444443    12111          11234455666777765    


Q ss_pred             CCChhHHHHHHHhccc-CChhhHHHHHHHHHh----cCCCCchHHHH----------HHHHHHHHhccc-----CChhhH
Q 040338          245 GGSTQKADLAFELMSR-RNMISWMVLISAFSQ----AGVLEKPRFFF----------FFVSLLSGCSHS-----GPVTKG  304 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~----~g~~~~a~~~~----------~~~~l~~~~~~~-----~~~~~a  304 (385)
                      .++.++|...|++..+ .+...+..+...|..    .+++++|+..+          .+..+...|...     ++.++|
T Consensus       236 ~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A  315 (490)
T 2xm6_A          236 TQDYTQSRVLFSQSAEQGNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQA  315 (490)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHH
Confidence            7899999999998876 466777788888877    78889999888          566677777766     899999


Q ss_pred             HHHHHHHHhccchhhHHHHHHHHHccC---CHHHHHHHHHhCCCCCCcchHHHHHHHHHh----cCChHHHHHHHHHHHh
Q 040338          305 KHYFTAMAKFTYTCYFVCMVDLLGLSG---LLGEAKKLIDEMPSKPTCVIWGALLGACCS----HYNTKLAELVMRNLLQ  377 (385)
Q Consensus       305 ~~~~~~~~~~~~~~~~~~li~~~~~~g---~~~~A~~~~~~m~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~  377 (385)
                      ...+++..+.+....+..+...|...|   ++++|.+.|++..+..+...+..|...|..    .+++++|..++++..+
T Consensus       316 ~~~~~~a~~~~~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~  395 (490)
T 2xm6_A          316 ISWYTKSAEQGDATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAE  395 (490)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHh
Confidence            999999999888777888888888766   789999999988877788889999999998    8999999999999988


Q ss_pred             ccc
Q 040338          378 LDV  380 (385)
Q Consensus       378 ~~~  380 (385)
                      .+.
T Consensus       396 ~~~  398 (490)
T 2xm6_A          396 QGL  398 (490)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            764

>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=99.55  E-value=2.9e-12  Score=126.90  Aligned_cols=339  Identities=12%  Similarity=0.001  Sum_probs=243.5

Q ss_pred             cccccCCChHHHHHHHHHHHHcccchhhHHh---------------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccC
Q 040338            2 KACGSLKSLPIARKIHAQLISTCLISSIFLQ---------------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVG   66 (385)
Q Consensus         2 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---------------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~   66 (385)
                      ++|...|.+.+|..+++.++-.   |+.|..               +........++....+   ..-+-..   |...|
T Consensus       993 Kaf~~aglp~EaieLLEKivl~---~s~fs~n~~LqnlLi~tAIkaD~~Rv~eyI~kLd~~d---~~eIA~I---ai~lg 1063 (1630)
T 1xi4_A          993 KAFMTADLPNELIELLEKIVLD---NSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYD---APDIANI---AISNE 1063 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHHHHcC---CCcccccHHHHHHHHHHHHHhChhhHHHHHHHhhhcc---HHHHHHH---HHhCC
Confidence            4567789999999999999843   332222               2333333333322222   2223333   23378


Q ss_pred             ChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccc-------cchHHHHHHhcCCCCCC
Q 040338           67 NIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK-------FGIIRLLIMFQKMPERD  139 (385)
Q Consensus        67 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~-------~~~~~a~~~~~~~~~~~  139 (385)
                      .+++|..+|++..     ......+.++.   ..+++++|.++.++...+.....-       |.+++|.+.|.+-  .|
T Consensus      1064 lyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aervn~p~vWsqLAKAql~~G~~kEAIdsYiKA--dD 1133 (1630)
T 1xi4_A         1064 LFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKA--DD 1133 (1630)
T ss_pred             CHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCHHHHHHHHHhc--CC
Confidence            8888888887752     12222233332   667888888888877554332111       8888888888663  67


Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDM  219 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  219 (385)
                      ...|..++.++.+.|++++|.+.|....+..  ++....+.+..+|++.+++++...+    ++   .++...+..+-..
T Consensus      1134 ~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~f----I~---~~n~ad~~~iGd~ 1204 (1630)
T 1xi4_A         1134 PSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEF----IN---GPNNAHIQQVGDR 1204 (1630)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHH----Hh---CCCHHHHHHHHHH
Confidence            7788999999999999999999999877754  4433344588899999888754433    22   3455666678888


Q ss_pred             HHhcCCCC----CCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH--------H
Q 040338          220 YLKCGCNG----IESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF--------F  287 (385)
Q Consensus       220 ~~~~g~~~----~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~--------~  287 (385)
                      |...|+++    .--....|..+...|.+.|++++|.+.+++.  .+..+|..+-.+|...|++..|....        .
T Consensus      1205 le~eg~YeeA~~~Y~kA~ny~rLA~tLvkLge~q~AIEaarKA--~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~de 1282 (1630)
T 1xi4_A         1205 CYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADE 1282 (1630)
T ss_pred             HHhcCCHHHHHHHHHhhhHHHHHHHHHHHhCCHHHHHHHHHHh--CCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHH
Confidence            88888766    2233468999999999999999999999977  56689999999999999999888776        6


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHc--cCCHHHHHHHHHhCCCC-------CCcchHHHHH
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGL--SGLLGEAKKLIDEMPSK-------PTCVIWGALL  356 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~--~g~~~~A~~~~~~m~~~-------p~~~~~~~li  356 (385)
                      +..++..|.+.|.+++|+.+++.......  ...|+-+...|++  -+++-++.++|..-..-       -+...|..++
T Consensus      1283 Leeli~yYe~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~~e~~~lW~elv 1362 (1630)
T 1xi4_A         1283 LEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELV 1362 (1630)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHHHHHHHHHHHHH
Confidence            77889999999999999999998877666  6677767777766  45677788887755542       3456799999


Q ss_pred             HHHHhcCChHHHHH
Q 040338          357 GACCSHYNTKLAEL  370 (385)
Q Consensus       357 ~~~~~~g~~~~a~~  370 (385)
                      -.|.+.|+++.|..
T Consensus      1363 ~LY~~~~e~dnA~~ 1376 (1630)
T 1xi4_A         1363 FLYDKYEEYDNAII 1376 (1630)
T ss_pred             HHHHhcccHHHHHH
Confidence            99999999999883

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.54  E-value=8.6e-14  Score=117.39  Aligned_cols=213  Identities=11%  Similarity=-0.100  Sum_probs=179.6

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC--CchHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS--LDVFVGSGLI  217 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~li  217 (385)
                      ...|..+...+...|++++|+..|++..+..  .+...+..+..++...|++++|.+.++...+....  ++..      
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~------   76 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYK------   76 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHH------
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchH------
Confidence            3567888899999999999999999999886  78889999999999999999999999998875421  1110      


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHH---------
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFF---------  286 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~---------  286 (385)
                                  ....++..+...+...|++++|...|++..+  |+.       ..+...|++++|+..+         
T Consensus        77 ------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~-------~~~~~~~~~~~a~~~~~~~~~~~~~  137 (258)
T 3uq3_A           77 ------------VISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTA-------DILTKLRNAEKELKKAEAEAYVNPE  137 (258)
T ss_dssp             ------------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCH-------HHHHHHHHHHHHHHHHHHHHHCCHH
T ss_pred             ------------HHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchh-------HHHHHHhHHHHHHHHHHHHHHcCcc
Confidence                        1135667788888899999999999998876  442       3455566677777776         


Q ss_pred             ---HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHH
Q 040338          287 ---FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGAC  359 (385)
Q Consensus       287 ---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~  359 (385)
                         .+..+...+...|++++|...++++.+..+  ...+..+...|.+.|++++|.+.|++..+. | +...|..+...|
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~  217 (258)
T 3uq3_A          138 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQ  217 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHH
Confidence               788899999999999999999999998877  788889999999999999999999988763 4 467899999999


Q ss_pred             HhcCChHHHHHHHHHHHhcc
Q 040338          360 CSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       360 ~~~g~~~~a~~~~~~~~~~~  379 (385)
                      ...|++++|...+++..+..
T Consensus       218 ~~~g~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          218 IAVKEYASALETLDAARTKD  237 (258)
T ss_dssp             HHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHhC
Confidence            99999999999999999887

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.53  E-value=6.4e-13  Score=113.16  Aligned_cols=232  Identities=9%  Similarity=-0.043  Sum_probs=159.6

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  166 (385)
                      ...+......+...|++++|+..|++..+.+                   +.+...+..+..++...|++++|+..+++.
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-------------------p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a   63 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-------------------YNSPYIYNRRAVCYYELAKYDLAQKDIETY   63 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-------------------CCCSTTHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-------------------CCcHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            3445556677778888888888887776554                   345557777888888888888888888888


Q ss_pred             HHCCCCCC--HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc
Q 040338          167 WNHGFGLS--SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE  244 (385)
Q Consensus       167 ~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~  244 (385)
                      .+.+..|+  ...|..+...+...|++++|++.++...+..+.                       +..++..+...|..
T Consensus        64 ~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~-----------------------~~~~~~~l~~~~~~  120 (272)
T 3u4t_A           64 FSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRDTT-----------------------RLDMYGQIGSYFYN  120 (272)
T ss_dssp             HTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-----------------------CTHHHHHHHHHHHH
T ss_pred             HhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCcc-----------------------cHHHHHHHHHHHHH
Confidence            77432222  233677777888888888888888888776431                       23345667777777


Q ss_pred             CCChhHHHHHHHhcccC---ChhhHHHHH-HHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hh
Q 040338          245 GGSTQKADLAFELMSRR---NMISWMVLI-SAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TC  318 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~~---~~~~~~~li-~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~  318 (385)
                      .|++++|+..|++..+.   +...+..+. ..|.                       .+++++|...++++.+..+  ..
T Consensus       121 ~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~-----------------------~~~~~~A~~~~~~a~~~~p~~~~  177 (272)
T 3u4t_A          121 KGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYY-----------------------NKEYVKADSSFVKVLELKPNIYI  177 (272)
T ss_dssp             TTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHH-----------------------TTCHHHHHHHHHHHHHHSTTCHH
T ss_pred             ccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHHHHhCccchH
Confidence            88888888888887752   333343333 2222                       2267777777777777666  55


Q ss_pred             hHHHHHHHHHccCC---HHHHHHHHHhCCCC----CCc------chHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          319 YFVCMVDLLGLSGL---LGEAKKLIDEMPSK----PTC------VIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       319 ~~~~li~~~~~~g~---~~~A~~~~~~m~~~----p~~------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .+..+...+...|+   +++|...+++..+.    |+.      .+|..+...|...|++++|...+++..+.+|.++
T Consensus       178 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~  255 (272)
T 3u4t_A          178 GYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILALDPTNK  255 (272)
T ss_dssp             HHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCccHH
Confidence            66667777777777   66677777666542    442      4677788888888999999999998888887653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.52  E-value=9.8e-12  Score=116.66  Aligned_cols=327  Identities=13%  Similarity=0.028  Sum_probs=209.2

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc--cccc---
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL--FCWK---  122 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~--~~~~---  122 (385)
                      |...|..++. +..   .|++++|..+|+.+.+. .+.+...|..++..+.+.|++++|..+|++.....+  ..|.   
T Consensus        12 ~~~~w~~l~~-~~~---~~~~~~a~~~~e~al~~-~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~   86 (530)
T 2ooe_A           12 DLDAWSILIR-EAQ---NQPIDKARKTYERLVAQ-FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYL   86 (530)
T ss_dssp             CHHHHHHHHH-HHH---SSCHHHHHHHHHHHHTT-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHH
T ss_pred             CHHHHHHHHH-HHH---hCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHH
Confidence            4556666665 233   56666666666666654 233455666666666666666666666666654332  1111   


Q ss_pred             -------cchHHHHH----HhcCC------CCCCcchHHHHHHHHHh---------CCCchHHHHHHHHHHHCCCCCC--
Q 040338          123 -------FGIIRLLI----MFQKM------PERDLVSWNTMISILTR---------HGFGFETLCTFIELWNHGFGLS--  174 (385)
Q Consensus       123 -------~~~~~a~~----~~~~~------~~~~~~~~~~li~~~~~---------~~~~~~a~~~~~~m~~~g~~p~--  174 (385)
                             |+.+.|.+    +|++.      ..++...|...+....+         .|+++.|..+|++..+.   |+  
T Consensus        87 ~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~---P~~~  163 (530)
T 2ooe_A           87 SYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVN---PMIN  163 (530)
T ss_dssp             HHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTS---CCTT
T ss_pred             HHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhc---hhhh
Confidence                   22222221    33221      22456678777776654         67889999999998772   33  


Q ss_pred             -HhhHHHHHHH---h----------cCccCccchhhHHHHHH------HhC---CCCc--------hHHHHHHHHHHHhc
Q 040338          175 -SMLYATAFSA---R----------ASVYDLEWGPHLHSRVV------HME---PSLD--------VFVGSGLIDMYLKC  223 (385)
Q Consensus       175 -~~t~~~ll~~---~----------~~~~~~~~a~~~~~~~~------~~~---~~~~--------~~~~~~li~~~~~~  223 (385)
                       ...|......   +          .+.+++..|..++..+.      +..   +.|+        ...|...+......
T Consensus       164 ~~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~  243 (530)
T 2ooe_A          164 IEQLWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSN  243 (530)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcC
Confidence             2333322221   1          12345556666555522      111   2332        23454444332221


Q ss_pred             C----CCC----------------CCchhhHHHHHHHHHHc-------CCChh-------HHHHHHHhccc---C-Chhh
Q 040338          224 G----CNG----------------IESSIQIGKALVTMYAE-------GGSTQ-------KADLAFELMSR---R-NMIS  265 (385)
Q Consensus       224 g----~~~----------------~~~~~~~~~~li~~~~~-------~g~~~-------~A~~~~~~m~~---~-~~~~  265 (385)
                      +    +..                .+.+...|......+.+       .|+++       +|..+|++..+   | +...
T Consensus       244 ~~~~~~~~~~~~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l  323 (530)
T 2ooe_A          244 PLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLL  323 (530)
T ss_dssp             SSCCSCSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHH
T ss_pred             CccCCcchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHH
Confidence            1    110                23356677777777765       79987       89999998864   4 5678


Q ss_pred             HHHHHHHHHhcCCCCchHHHH-------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHH-HHc
Q 040338          266 WMVLISAFSQAGVLEKPRFFF-------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDL-LGL  329 (385)
Q Consensus       266 ~~~li~~~~~~g~~~~a~~~~-------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~-~~~  329 (385)
                      |..++..+.+.|++++|..++             .|...+..+.+.|++++|..+|++..+.++  ...+...... +..
T Consensus       324 ~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~  403 (530)
T 2ooe_A          324 YFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYC  403 (530)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHH
Confidence            888999999999999999988             577777777889999999999999988766  2333222222 336


Q ss_pred             cCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          330 SGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       330 ~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .|+.++|.++|+...+. | +...|..++..+.+.|+.++|..+|++.+..++.+
T Consensus       404 ~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~  458 (530)
T 2ooe_A          404 SKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  458 (530)
T ss_dssp             TCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSC
T ss_pred             cCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCC
Confidence            89999999999988764 5 56789999999999999999999999999876543

>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=99.50  E-value=2.2e-12  Score=110.07  Aligned_cols=217  Identities=10%  Similarity=-0.100  Sum_probs=180.0

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC----ccCccchhhHHHHHHHhCCCCchHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS----VYDLEWGPHLHSRVVHMEPSLDVFVG  213 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  213 (385)
                      .+..++..+...+...|++++|+..|++..+.   -+...+..+...+..    .+++++|...+++..+.+   +..  
T Consensus         4 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~--   75 (273)
T 1ouv_A            4 QDPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSN--   75 (273)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHH--
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHH--
Confidence            35667788888899999999999999998873   345667777778888    899999999999988775   233  


Q ss_pred             HHHHHHHHhcCCCCCCchhhHHHHHHHHHHc----CCChhHHHHHHHhcccC-ChhhHHHHHHHHHh----cCCCCchHH
Q 040338          214 SGLIDMYLKCGCNGIESSIQIGKALVTMYAE----GGSTQKADLAFELMSRR-NMISWMVLISAFSQ----AGVLEKPRF  284 (385)
Q Consensus       214 ~~li~~~~~~g~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~----~g~~~~a~~  284 (385)
                                          .+..+...|..    .+++++|+..|++..+. +...+..+...|..    .+++++|+.
T Consensus        76 --------------------a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~  135 (273)
T 1ouv_A           76 --------------------GCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVE  135 (273)
T ss_dssp             --------------------HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             --------------------HHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHH
Confidence                                33555666666    78999999999887664 66788888888888    889999998


Q ss_pred             HH----------HHHHHHHHhcc----cCChhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCC
Q 040338          285 FF----------FFVSLLSGCSH----SGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       285 ~~----------~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~  346 (385)
                      .+          ++..+...|..    .+++++|...+++..+.+....+..+...|..    .+++++|.+.|++..+.
T Consensus       136 ~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~  215 (273)
T 1ouv_A          136 YFTKACDLNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACEL  215 (273)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhC
Confidence            88          66777777777    89999999999999988888888889999999    99999999999988776


Q ss_pred             CCcchHHHHHHHHHh----cCChHHHHHHHHHHHhccccC
Q 040338          347 PTCVIWGALLGACCS----HYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       347 p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .+...+..+...|..    .+++++|...+++..+.++.+
T Consensus       216 ~~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~  255 (273)
T 1ouv_A          216 ENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAKG  255 (273)
T ss_dssp             TCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             CCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcCCHH
Confidence            557788889999999    999999999999999988764

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.49  E-value=1.9e-12  Score=109.06  Aligned_cols=221  Identities=9%  Similarity=-0.034  Sum_probs=168.9

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ..|..+-..+..   .|++++|...++...+..  .+..++..+..+|...|++++|.+.|++..+.+.           
T Consensus         6 ~~~~~~g~~~~~---~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-----------   69 (258)
T 3uq3_A            6 DKEKAEGNKFYK---ARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGR-----------   69 (258)
T ss_dssp             HHHHHHHHHHHH---TTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----------
T ss_pred             HHHHHHHHHHHH---hccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCc-----------
Confidence            355666666555   899999999999999987  7899999999999999999999999988755332           


Q ss_pred             HHhcCCCCCC----cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          130 IMFQKMPERD----LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       130 ~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                          .. .++    ..+|..+...+...|++++|...|++..+.  .|+.       ..+.+.|++++|...++.+....
T Consensus        70 ----~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~~  135 (258)
T 3uq3_A           70 ----EM-RADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYVN  135 (258)
T ss_dssp             ----HT-TCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             ----cc-ccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHcC
Confidence                00 112    578889999999999999999999999885  4553       34556688999999999988753


Q ss_pred             CCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCch
Q 040338          206 PSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKP  282 (385)
Q Consensus       206 ~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a  282 (385)
                      +                       .+...+..+...+...|++++|...|++..+  | +...+..              
T Consensus       136 ~-----------------------~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~--------------  178 (258)
T 3uq3_A          136 P-----------------------EKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSN--------------  178 (258)
T ss_dssp             H-----------------------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH--------------
T ss_pred             c-----------------------chHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHH--------------
Confidence            2                       2334567778888889999999999998875  2 3334444              


Q ss_pred             HHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          283 RFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       283 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                              +...+...|++++|...+++..+..+  ...+..+...+.+.|++++|.+.|++..+
T Consensus       179 --------l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  235 (258)
T 3uq3_A          179 --------RAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALETLDAART  235 (258)
T ss_dssp             --------HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --------HHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                    44445555666677777777766666  67777788888888888888888877654

>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=99.48  E-value=5e-12  Score=112.80  Aligned_cols=234  Identities=8%  Similarity=-0.002  Sum_probs=187.0

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCC-chHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGF-GFETLCTFIE  165 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~  165 (385)
                      ...|..+..++.+.|++++|++.|++..+.+                   +.+..+|+.+..++...|+ +++|+..|++
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-------------------P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~  157 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-------------------AANYTVWHFRRVLLKSLQKDLHEEMNYITA  157 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-------------------ccCHHHHHHHHHHHHHcccCHHHHHHHHHH
Confidence            4567788888889999999999999887655                   3567889999999999997 9999999999


Q ss_pred             HHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc
Q 040338          166 LWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE  244 (385)
Q Consensus       166 m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~  244 (385)
                      ..+.  .| +...|..+-.++...|++++|+..++.+++..+                       .+...|..+..++.+
T Consensus       158 al~l--~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP-----------------------~~~~a~~~lg~~~~~  212 (382)
T 2h6f_A          158 IIEE--QPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDA-----------------------KNYHAWQHRQWVIQE  212 (382)
T ss_dssp             HHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-----------------------TCHHHHHHHHHHHHH
T ss_pred             HHHH--CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCc-----------------------cCHHHHHHHHHHHHH
Confidence            9885  44 677888888899999999999999999998754                       244556777778888


Q ss_pred             CCChhHHHHHHHhccc--C-ChhhHHHHHHHHHh-cCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hh
Q 040338          245 GGSTQKADLAFELMSR--R-NMISWMVLISAFSQ-AGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TC  318 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~-~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~  318 (385)
                      .|++++|+..|+++.+  | +...|+.+..++.. .|..++|+                 .+.+...+++.....+  ..
T Consensus       213 ~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~-----------------~~~el~~~~~Al~l~P~~~~  275 (382)
T 2h6f_A          213 FKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAV-----------------LEREVQYTLEMIKLVPHNES  275 (382)
T ss_dssp             HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHH-----------------HHHHHHHHHHHHHHSTTCHH
T ss_pred             cCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHH-----------------HHHHHHHHHHHHHHCCCCHH
Confidence            8899999999999876  3 66788888888888 55556663                 3444577777777776  77


Q ss_pred             hHHHHHHHHHccC--CHHHHHHHHHhCCCCC-CcchHHHHHHHHHhcC--------C-hHHHHHHHHHH-Hhcccc
Q 040338          319 YFVCMVDLLGLSG--LLGEAKKLIDEMPSKP-TCVIWGALLGACCSHY--------N-TKLAELVMRNL-LQLDVK  381 (385)
Q Consensus       319 ~~~~li~~~~~~g--~~~~A~~~~~~m~~~p-~~~~~~~li~~~~~~g--------~-~~~a~~~~~~~-~~~~~~  381 (385)
                      .|..+...+...|  ++++|.+.++++...| +...+..+...|.+.|        + .++|+++++++ .+.+|.
T Consensus       276 a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l~~~~DP~  351 (382)
T 2h6f_A          276 AWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTI  351 (382)
T ss_dssp             HHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhCch
Confidence            8888888888888  6899999999883334 4567888888888874        2 58999999999 777764

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.47  E-value=5.2e-13  Score=120.95  Aligned_cols=256  Identities=10%  Similarity=-0.061  Sum_probs=196.8

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCc----chHHHHHHHHHhCCCchHHHHHH
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDL----VSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                      ..+..+...+...|++++|...|++..+.+                   +.+.    ..|..+...|...|++++|...+
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-------------------~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~  109 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAG-------------------TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYH  109 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhc-------------------ccChhHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            345556678888999999999998876543                   2232    46888889999999999999999


Q ss_pred             HHHHHC----CCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHH
Q 040338          164 IELWNH----GFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKAL  238 (385)
Q Consensus       164 ~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~l  238 (385)
                      ++..+.    +-.| ...++..+...+...|++++|...+++..+.......                 ......++..+
T Consensus       110 ~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-----------------~~~~~~~~~~l  172 (411)
T 4a1s_A          110 KHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGD-----------------RLSEGRALYNL  172 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-----------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc-----------------hHHHHHHHHHH
Confidence            987653    2223 4567778888999999999999999988764211000                 01123355667


Q ss_pred             HHHHHcCCC-----------------hhHHHHHHHhccc-----C----ChhhHHHHHHHHHhcCCCCchHHHH------
Q 040338          239 VTMYAEGGS-----------------TQKADLAFELMSR-----R----NMISWMVLISAFSQAGVLEKPRFFF------  286 (385)
Q Consensus       239 i~~~~~~g~-----------------~~~A~~~~~~m~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~------  286 (385)
                      ...|...|+                 +++|+..+++..+     .    ...++..+...|...|++++|+..+      
T Consensus       173 ~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  252 (411)
T 4a1s_A          173 GNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRI  252 (411)
T ss_dssp             HHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            777777778                 8888888876543     1    2347778888899999999998888      


Q ss_pred             ------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC
Q 040338          287 ------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       287 ------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  346 (385)
                                  ++..+...+...|++++|...+++......        ...+..+...|...|++++|.+.+++....
T Consensus       253 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  332 (411)
T 4a1s_A          253 AREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAI  332 (411)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence                        678888999999999999999998876544        567788899999999999999999887652


Q ss_pred             ----CC----cchHHHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          347 ----PT----CVIWGALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       347 ----p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                          ++    ..++..+...|...|++++|...+++..+..
T Consensus       333 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  373 (411)
T 4a1s_A          333 AQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQLA  373 (411)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence                22    3478889999999999999999999987643

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.46  E-value=2.1e-12  Score=106.35  Aligned_cols=191  Identities=14%  Similarity=-0.013  Sum_probs=149.5

Q ss_pred             CChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           47 RYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        47 ~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                      ++...+..+-..+..   .|++++|...++...+.. +.+...+..+..++.+.|++++|+..|++..+.+         
T Consensus         3 ~~~~~~~~lg~~~~~---~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~---------   69 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYA---LGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART---------   69 (217)
T ss_dssp             -CCHHHHHHHHHHHH---TTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------
T ss_pred             CcHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC---------
Confidence            455566777777666   899999999999999875 4477889999999999999999999999887655         


Q ss_pred             HHHHHhcCCCCCCcchHHHHHHHHHhC-----------CCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccch
Q 040338          127 RLLIMFQKMPERDLVSWNTMISILTRH-----------GFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWG  194 (385)
Q Consensus       127 ~a~~~~~~~~~~~~~~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a  194 (385)
                                +.+...+..+...+.+.           |++++|+..|++..+.  .| +...+..+..++...|++++|
T Consensus        70 ----------P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A  137 (217)
T 2pl2_A           70 ----------PRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKA  137 (217)
T ss_dssp             ----------TTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             ----------CCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHH
Confidence                      35677899999999999           9999999999999885  45 567788888999999999999


Q ss_pred             hhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHH
Q 040338          195 PHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLIS  271 (385)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~  271 (385)
                      +..+++.++..  .+...+                      ..+...|...|++++|+..|++..+  | +...+..+..
T Consensus       138 ~~~~~~al~~~--~~~~~~----------------------~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~  193 (217)
T 2pl2_A          138 EASLKQALALE--DTPEIR----------------------SALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYAS  193 (217)
T ss_dssp             HHHHHHHHHHC--CCHHHH----------------------HHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHhcc--cchHHH----------------------HHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHH
Confidence            99999999887  444444                      5666677777899999999998875  4 5677888888


Q ss_pred             HHHhcCCCCchHHHH
Q 040338          272 AFSQAGVLEKPRFFF  286 (385)
Q Consensus       272 ~~~~~g~~~~a~~~~  286 (385)
                      .+...|++++|+..+
T Consensus       194 ~~~~~g~~~~A~~~~  208 (217)
T 2pl2_A          194 ALLLKGKAEEAARAA  208 (217)
T ss_dssp             HHTC-----------
T ss_pred             HHHHccCHHHHHHHH
Confidence            888888888887654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.46  E-value=6.2e-13  Score=113.34  Aligned_cols=240  Identities=8%  Similarity=-0.167  Sum_probs=153.3

Q ss_pred             cCChHHHHHHHHHHHHhcc---CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcc
Q 040338           65 VGNIKMALHLHGLVKKFYF---VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLV  141 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~  141 (385)
                      .|++++|+..++.+.+...   +.+..++..+...|...|++++|...|++..+.+                   +.+..
T Consensus        18 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-------------------~~~~~   78 (275)
T 1xnf_A           18 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-------------------PDMPE   78 (275)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------CCCHH
T ss_pred             cchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-------------------CCcHH
Confidence            5777888888888777532   1245667777778888888888888887765544                   34567


Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYL  221 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  221 (385)
                      +|..+...+...|++++|...|++..+.. +.+...+..+...+.+.|++++|...++.+.+..+.  ....        
T Consensus        79 ~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~--~~~~--------  147 (275)
T 1xnf_A           79 VFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPN--DPFR--------  147 (275)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHH--------
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC--ChHH--------
Confidence            77778888888888888888888877642 224667777777788888888888888887776432  1111        


Q ss_pred             hcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccC
Q 040338          222 KCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSG  299 (385)
Q Consensus       222 ~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~  299 (385)
                                    ...+..+...|++++|...++....  |+......                      ++..+...+
T Consensus       148 --------------~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~----------------------~~~~~~~~~  191 (275)
T 1xnf_A          148 --------------SLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWN----------------------IVEFYLGNI  191 (275)
T ss_dssp             --------------HHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHH----------------------HHHHHTTSS
T ss_pred             --------------HHHHHHHHHhcCHHHHHHHHHHHHhcCCcchHHHH----------------------HHHHHHHhc
Confidence                          1122222344678888888866543  21111111                      223333444


Q ss_pred             ChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHhcCChHHHHHHH
Q 040338          300 PVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      +.++|...++......+      ...+..+...|.+.|++++|.+.|++.... |+.  +.....++...|++++|++.+
T Consensus       192 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~--~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          192 SEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHN--FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             CHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTT--CHHHHHHHHHHHHHHHC----
T ss_pred             CHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchh--HHHHHHHHHHHHHHHhhHHHH
Confidence            55566666666655444      466777888888888899998888888764 432  334455677778888887765

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.46  E-value=6e-13  Score=116.54  Aligned_cols=256  Identities=11%  Similarity=-0.043  Sum_probs=188.7

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC----cchHHHHHHHHHhCCCchHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD----LVSWNTMISILTRHGFGFETLCTFI  164 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~  164 (385)
                      .+......+...|++++|...|++..+.+                   +.+    ...+..+...+...|++++|...++
T Consensus         7 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~-------------------~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~   67 (338)
T 3ro2_A            7 ELALEGERLCKSGDCRAGVSFFEAAVQVG-------------------TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHH   67 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhhC-------------------cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            34455667778899999999988775533                   122    3567788889999999999999988


Q ss_pred             HHHHC----CCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC-CchHHHHHHHHHHHhcCCCCCCchhhHHHHH
Q 040338          165 ELWNH----GFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS-LDVFVGSGLIDMYLKCGCNGIESSIQIGKAL  238 (385)
Q Consensus       165 ~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~~~~~~~~~~l  238 (385)
                      +..+.    +..| ...++..+...+...|++++|...+++..+.... ++..                  ....++..+
T Consensus        68 ~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~------------------~~~~~~~~l  129 (338)
T 3ro2_A           68 HDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKV------------------GEARALYNL  129 (338)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH------------------HHHHHHHHH
T ss_pred             HHHHHhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCch------------------HHHHHHHHH
Confidence            86543    2222 2556777888888999999999999887764221 1110                  112244556


Q ss_pred             HHHHHcCCC--------------------hhHHHHHHHhccc-----C----ChhhHHHHHHHHHhcCCCCchHHHH---
Q 040338          239 VTMYAEGGS--------------------TQKADLAFELMSR-----R----NMISWMVLISAFSQAGVLEKPRFFF---  286 (385)
Q Consensus       239 i~~~~~~g~--------------------~~~A~~~~~~m~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~---  286 (385)
                      ...+...|+                    +++|...+++..+     +    ...++..+...+...|++++|+..+   
T Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  209 (338)
T 3ro2_A          130 GNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQR  209 (338)
T ss_dssp             HHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            666666667                    7777777766543     1    2346777888888899999888888   


Q ss_pred             ---------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhC
Q 040338          287 ---------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEM  343 (385)
Q Consensus       287 ---------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m  343 (385)
                                     ++..+...+...|++++|...+++......        ...+..+...+...|++++|.+.+++.
T Consensus       210 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  289 (338)
T 3ro2_A          210 LLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKH  289 (338)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence                           677888888999999999999998776433        557778889999999999999999887


Q ss_pred             CCC----CC----cchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          344 PSK----PT----CVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       344 ~~~----p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ...    ++    ..++..+...|...|++++|...+++..+....
T Consensus       290 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~  335 (338)
T 3ro2_A          290 LAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISRE  335 (338)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC---
T ss_pred             HHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHh
Confidence            652    22    447888999999999999999999999876543

>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=99.46  E-value=8.9e-12  Score=104.76  Aligned_cols=200  Identities=10%  Similarity=-0.075  Sum_probs=160.1

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDM  219 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  219 (385)
                      ...|..+...+...|++++|...|+++.+.. +.+...+..+...+...|++++|.+.++++.+....            
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~------------  103 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR------------  103 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------------
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC------------
Confidence            5678888899999999999999999998762 336778888999999999999999999999887532            


Q ss_pred             HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcc
Q 040338          220 YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSH  297 (385)
Q Consensus       220 ~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~  297 (385)
                                 +...+..+...+...|++++|+..|++..+  .+..                   ....+..+...+..
T Consensus       104 -----------~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~-------------------~~~~~~~la~~~~~  153 (252)
T 2ho1_A          104 -----------NARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPE-------------------RSRVFENLGLVSLQ  153 (252)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTT-------------------HHHHHHHHHHHHHH
T ss_pred             -----------cHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcc-------------------cHHHHHHHHHHHHH
Confidence                       233456777788888999999999998875  1110                   00133444555566


Q ss_pred             cCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHH
Q 040338          298 SGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMR  373 (385)
Q Consensus       298 ~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~  373 (385)
                      .|++++|...++++.+..+  ...+..+...+...|++++|...++++.+.  .+...+..+...+...|++++|.+.++
T Consensus       154 ~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~  233 (252)
T 2ho1_A          154 MKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGL  233 (252)
T ss_dssp             TTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            6777888888888877666  777888999999999999999999998764  456678888899999999999999999


Q ss_pred             HHHhccccC
Q 040338          374 NLLQLDVKV  382 (385)
Q Consensus       374 ~~~~~~~~~  382 (385)
                      ++.+..|..
T Consensus       234 ~~~~~~p~~  242 (252)
T 2ho1_A          234 QLKRLYPGS  242 (252)
T ss_dssp             HHHHHCTTS
T ss_pred             HHHHHCCCC
Confidence            999887764

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.45  E-value=9e-13  Score=118.90  Aligned_cols=131  Identities=11%  Similarity=-0.043  Sum_probs=96.3

Q ss_pred             hhHHHHHHHhccc-----C----ChhhHHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCC
Q 040338          248 TQKADLAFELMSR-----R----NMISWMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGP  300 (385)
Q Consensus       248 ~~~A~~~~~~m~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~  300 (385)
                      +++|...+++..+     +    ...++..+...|...|++++|+..+                  ++..+...+...|+
T Consensus       163 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~  242 (406)
T 3sf4_A          163 LQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGE  242 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCC
Confidence            6666666554432     1    1245666667777777777777666                  67777778888888


Q ss_pred             hhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CC----cchHHHHHHHHHhcCC
Q 040338          301 VTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PT----CVIWGALLGACCSHYN  364 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~----~~~~~~li~~~~~~g~  364 (385)
                      +++|...+++......        ..++..+...|...|++++|.+.+++....    ++    ..++..+...|...|+
T Consensus       243 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~  322 (406)
T 3sf4_A          243 FETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGN  322 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCC
Confidence            8888888888765433        557778888899999999999998877552    22    4577888889999999


Q ss_pred             hHHHHHHHHHHHhc
Q 040338          365 TKLAELVMRNLLQL  378 (385)
Q Consensus       365 ~~~a~~~~~~~~~~  378 (385)
                      +++|...+++..+.
T Consensus       323 ~~~A~~~~~~al~~  336 (406)
T 3sf4_A          323 HDQAMHFAEKHLEI  336 (406)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999987764

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.44  E-value=1.5e-12  Score=117.87  Aligned_cols=250  Identities=12%  Similarity=-0.056  Sum_probs=192.3

Q ss_pred             hccCChHHHHHHHHHHHHhccCCCc----hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCC--
Q 040338           63 LCVGNIKMALHLHGLVKKFYFVSDE----SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMP--  136 (385)
Q Consensus        63 ~~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~--  136 (385)
                      ...|++++|...+++..+.+.. +.    .++..+...|...|++++|...|++..+               +.....  
T Consensus        59 ~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---------------~~~~~~~~  122 (411)
T 4a1s_A           59 CNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLT---------------LAKSMNDR  122 (411)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---------------HHHHTTCH
T ss_pred             HHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---------------HHHHccCc
Confidence            3389999999999999987422 33    4788899999999999999999977532               222221  


Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC----CCCC-CHhhHHHHHHHhcCccC-----------------ccch
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNH----GFGL-SSMLYATAFSARASVYD-----------------LEWG  194 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~-----------------~~~a  194 (385)
                      +....++..+...|...|++++|...+++..+.    +-.| ...++..+...+...|+                 +++|
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            124567888899999999999999999987653    2122 34577888889999999                 8888


Q ss_pred             hhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----CC----hhh
Q 040338          195 PHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----RN----MIS  265 (385)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~~----~~~  265 (385)
                      .+.+++..+....               .++  ......++..+...|...|++++|+..+++..+     ++    ..+
T Consensus       203 ~~~~~~al~~~~~---------------~~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  265 (411)
T 4a1s_A          203 VEFYQENLKLMRD---------------LGD--RGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRA  265 (411)
T ss_dssp             HHHHHHHHHHHHH---------------HTC--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHH---------------cCC--HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHH
Confidence            8888776543110               000  011234667788889999999999999988765     12    237


Q ss_pred             HHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhh
Q 040338          266 WMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCY  319 (385)
Q Consensus       266 ~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~  319 (385)
                      +..+...|...|++++|+..+                  ++..+...+...|++++|...+++......        ...
T Consensus       266 ~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  345 (411)
T 4a1s_A          266 NSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARA  345 (411)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHH
Confidence            888899999999999999888                  677888899999999999999998877543        457


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      +..+...|.+.|++++|.+.|++..+
T Consensus       346 ~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          346 CWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            88899999999999999999987654

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.43  E-value=4.3e-12  Score=104.41  Aligned_cols=195  Identities=15%  Similarity=-0.015  Sum_probs=145.5

Q ss_pred             CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHH
Q 040338           84 VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus        84 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                      +++...+..+...+.+.|++++|...|++..+.+                   +.+...|..+...+.+.|++++|+..|
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~a~~~lg~~~~~~g~~~~A~~~~   62 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-------------------PQDPEALYWLARTQLKLGLVNPALENG   62 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-------------------SSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            5678889999999999999999999999988776                   467888999999999999999999999


Q ss_pred             HHHHHCCCCC-CHhhHHHHHHHhcCc-----------cCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCch
Q 040338          164 IELWNHGFGL-SSMLYATAFSARASV-----------YDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESS  231 (385)
Q Consensus       164 ~~m~~~g~~p-~~~t~~~ll~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~  231 (385)
                      ++..+.  .| +...+..+..++...           |++++|+..++..++..+.                       +
T Consensus        63 ~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~-----------------------~  117 (217)
T 2pl2_A           63 KTLVAR--TPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPR-----------------------Y  117 (217)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTT-----------------------C
T ss_pred             HHHHHh--CCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcc-----------------------c
Confidence            999885  45 567888888899999           9999999999999887532                       3


Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhcccC--ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSRR--NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFT  309 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~  309 (385)
                      ...+..+...+...|++++|+..|++..+-  +...+                      ..+..++...|++++|...++
T Consensus       118 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~----------------------~~la~~~~~~g~~~~A~~~~~  175 (217)
T 2pl2_A          118 APLHLQRGLVYALLGERDKAEASLKQALALEDTPEIR----------------------SALAELYLSMGRLDEALAQYA  175 (217)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHH----------------------HHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHH----------------------HHHHHHHHHcCCHHHHHHHHH
Confidence            345567778888899999999999887642  23333                      344455566667778888888


Q ss_pred             HHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          310 AMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       310 ~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      +..+..+  ...+..+...+.+.|++++|.+.|++.-
T Consensus       176 ~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          176 KALEQAPKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHTC---------------
T ss_pred             HHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            8888777  7778888999999999999999887653

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.43  E-value=2.3e-12  Score=109.82  Aligned_cols=148  Identities=8%  Similarity=-0.138  Sum_probs=98.2

Q ss_pred             hhhhHHHHHhhhCCC-------ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhH
Q 040338           33 LIDDDYRVFCDIGPR-------YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDY  105 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~-------~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~  105 (385)
                      ++++|...|+++...       +...|..+...+..   .|++++|...+++..+.. +.+..++..+...|...|++++
T Consensus        20 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           20 QQEVILARMEQILASRALTDDERAQLLYERGVLYDS---LGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHH
T ss_pred             hHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHH---cccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHH
Confidence            455555555544321       23455556666555   788888888888877764 3356777778888888888888


Q ss_pred             HHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHh
Q 040338          106 AESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSAR  185 (385)
Q Consensus       106 a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  185 (385)
                      |.+.|++..+.+                   +.+..++..+...+.+.|++++|...|+++.+.  .|+.......+..+
T Consensus        96 A~~~~~~al~~~-------------------~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~  154 (275)
T 1xnf_A           96 AYEAFDSVLELD-------------------PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLA  154 (275)
T ss_dssp             HHHHHHHHHHHC-------------------TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-------------------ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHH
Confidence            888887765543                   345667777777888888888888888887764  44444444444455


Q ss_pred             cCccCccchhhHHHHHHHhC
Q 040338          186 ASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       186 ~~~~~~~~a~~~~~~~~~~~  205 (385)
                      ...|++++|...++......
T Consensus       155 ~~~~~~~~A~~~~~~~~~~~  174 (275)
T 1xnf_A          155 EQKLDEKQAKEVLKQHFEKS  174 (275)
T ss_dssp             HHHHCHHHHHHHHHHHHHHS
T ss_pred             HHhcCHHHHHHHHHHHHhcC
Confidence            66677788888877766654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.43  E-value=5.4e-12  Score=113.78  Aligned_cols=267  Identities=10%  Similarity=-0.066  Sum_probs=202.9

Q ss_pred             cCChHHHHHHHHHHHHhccCCC----chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC--C
Q 040338           65 VGNIKMALHLHGLVKKFYFVSD----ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE--R  138 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~--~  138 (385)
                      .|++++|...+++..+.+.. +    ..++..+...|...|++++|...+++...               +......  .
T Consensus        22 ~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~---------------~~~~~~~~~~   85 (406)
T 3sf4_A           22 SGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLT---------------LARTIGDQLG   85 (406)
T ss_dssp             TTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHH
T ss_pred             hccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---------------HHHhccccHH
Confidence            89999999999999987422 3    35788889999999999999999876532               2222211  2


Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCC----CCC-CHhhHHHHHHHhcCccC--------------------ccc
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHG----FGL-SSMLYATAFSARASVYD--------------------LEW  193 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g----~~p-~~~t~~~ll~~~~~~~~--------------------~~~  193 (385)
                      ...++..+...+...|++++|...+++..+..    -.+ ...++..+...+...|+                    +++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            35578888899999999999999999886531    111 14477788888999999                    888


Q ss_pred             hhhHHHHHHHhCCC-CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----CC----h
Q 040338          194 GPHLHSRVVHMEPS-LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----RN----M  263 (385)
Q Consensus       194 a~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~~----~  263 (385)
                      |...++...+.... ++.                  .....++..+...|...|++++|...+++..+     ++    .
T Consensus       166 A~~~~~~al~~~~~~~~~------------------~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  227 (406)
T 3sf4_A          166 AVDFYEENLSLVTALGDR------------------AAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAER  227 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCH------------------HHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccCc------------------HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHH
Confidence            88888776653110 011                  11234567778888889999999999988764     22    2


Q ss_pred             hhHHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------h
Q 040338          264 ISWMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------T  317 (385)
Q Consensus       264 ~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~  317 (385)
                      .++..+...|...|++++|+..+                  ++..+...+...|++++|...+++..+...        .
T Consensus       228 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  307 (406)
T 3sf4_A          228 RAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEG  307 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHH
Confidence            37888889999999999999888                  677888899999999999999998876533        5


Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCCC--------CCcchHHHHHHHHHhcCCh
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPSK--------PTCVIWGALLGACCSHYNT  365 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~--------p~~~~~~~li~~~~~~g~~  365 (385)
                      ..+..+...|...|++++|.+.+++..+.        ....++..+...+...|+.
T Consensus       308 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          308 RACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence            57778899999999999999999887541        1244677788888887766

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.42  E-value=1e-11  Score=113.98  Aligned_cols=327  Identities=7%  Similarity=-0.113  Sum_probs=171.3

Q ss_pred             ccCCChHHHHHHHHHHHHcccchhhHHh-----------hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhc--cCChHHH
Q 040338            5 GSLKSLPIARKIHAQLISTCLISSIFLQ-----------LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLC--VGNIKMA   71 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~--~~~~~~a   71 (385)
                      .+.|+++.|...++++...|..+..+.-           ++++|...|++....++..+..+-..+.....  .+++++|
T Consensus        14 ~~~g~~~~A~~~~~~aa~~g~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~~~~~~A   93 (452)
T 3e4b_A           14 LKRGDTVTAQQNYQQLAELGYSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGATEAEHHEA   93 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCCTGGGTCC----------------------------CHHHHHHHHHTC--CCHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCcCHHHH
Confidence            3568899999999999887743332221           44899999988775566666655553333110  1478899


Q ss_pred             HHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHH---HHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHH
Q 040338           72 LHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYA---ESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMIS  148 (385)
Q Consensus        72 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a---~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~  148 (385)
                      ...|+...+.|.   ...+..|...|...+..+++   .+.+......                     .+...+..|..
T Consensus        94 ~~~~~~Aa~~g~---~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~---------------------g~~~a~~~Lg~  149 (452)
T 3e4b_A           94 ESLLKKAFANGE---GNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAA---------------------GYPEAGLAQVL  149 (452)
T ss_dssp             HHHHHHHHHTTC---SSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHH---------------------TCTTHHHHHHH
T ss_pred             HHHHHHHHHCCC---HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHC---------------------CCHHHHHHHHH
Confidence            999999988663   33677788888776654433   3333332221                     23445556666


Q ss_pred             HHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc---CccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 040338          149 ILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVY---DLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGC  225 (385)
Q Consensus       149 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  225 (385)
                      .|...+.++++........+.-...+...+..+...|...|   +.++|.+.|+...+.|.. +...+            
T Consensus       150 ~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~-~a~~~------------  216 (452)
T 3e4b_A          150 LYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTV-TAQRV------------  216 (452)
T ss_dssp             HHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCS-CHHHH------------
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCH-HHHHH------------
Confidence            66666655555444333332222223335555666666666   667777777777666542 22211            


Q ss_pred             CCCCchhhHHHHHHHHHHcC----CChhHHHHHHHhcccCChhhHHHHHHH-H--HhcCCCCchHHHH----------HH
Q 040338          226 NGIESSIQIGKALVTMYAEG----GSTQKADLAFELMSRRNMISWMVLISA-F--SQAGVLEKPRFFF----------FF  288 (385)
Q Consensus       226 ~~~~~~~~~~~~li~~~~~~----g~~~~A~~~~~~m~~~~~~~~~~li~~-~--~~~g~~~~a~~~~----------~~  288 (385)
                                ..+...|...    ++.++|+..|++....+...+..|... |  ...+++++|+..|          ++
T Consensus       217 ----------~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~  286 (452)
T 3e4b_A          217 ----------DSVARVLGDATLGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAE  286 (452)
T ss_dssp             ----------HHHHHHHTCGGGSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             ----------HHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHH
Confidence                      2222233222    456666666665552244455555544 2  3455555666555          34


Q ss_pred             HHHHHHhcccC-----ChhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCCCCcchHHHHHHHH
Q 040338          289 VSLLSGCSHSG-----PVTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSKPTCVIWGALLGAC  359 (385)
Q Consensus       289 ~~l~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~~  359 (385)
                      ..+...|. .|     +.++|...|++.. .+.+.....|...|..    ..++++|.+.|+...+..+......|...|
T Consensus       287 ~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y  364 (452)
T 3e4b_A          287 LLLGKLYY-EGKWVPADAKAAEAHFEKAV-GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQNSADFAIAQLF  364 (452)
T ss_dssp             HHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChHHHHHHHHHHH
Confidence            44444443 33     6666666666666 4445555555555554    336666777766665554555555565555


Q ss_pred             Hh----cCChHHHHHHHHHHHhccc
Q 040338          360 CS----HYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       360 ~~----~g~~~~a~~~~~~~~~~~~  380 (385)
                      ..    ..+.++|..+++...+.|.
T Consensus       365 ~~G~g~~~d~~~A~~~~~~A~~~g~  389 (452)
T 3e4b_A          365 SQGKGTKPDPLNAYVFSQLAKAQDT  389 (452)
T ss_dssp             HSCTTBCCCHHHHHHHHHHHHTTCC
T ss_pred             HhCCCCCCCHHHHHHHHHHHHHCCC
Confidence            53    3466666666666665554

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.42  E-value=2.3e-12  Score=107.67  Aligned_cols=199  Identities=12%  Similarity=0.005  Sum_probs=141.3

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      .....|..+...+...|++++|...|+++.+. .+.+...+..+...+...|++++|...++.+.+...           
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~-~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-----------   88 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEE-NKEDAIPYINFANLLSSVNELERALAFYDKALELDS-----------   88 (243)
T ss_dssp             ---------------------CCTTHHHHHTT-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-----------
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHh-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-----------
Confidence            45667888888899999999999999999874 344678888888899999999999999999887743           


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSG  294 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~  294 (385)
                                  .+..++..+...+...|++++|...+++..+  | +...+.                      .+...
T Consensus        89 ------------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~----------------------~~a~~  134 (243)
T 2q7f_A           89 ------------SAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFY----------------------MLGTV  134 (243)
T ss_dssp             ------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHH----------------------HHHHH
T ss_pred             ------------cchHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHH----------------------HHHHH
Confidence                        2345678889999999999999999988765  2 333333                      34445


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHH
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      +...|++++|...++++.+..+  ...+..+...+.+.|++++|.+.|++....  .+..+|..+...|...|++++|..
T Consensus       135 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  214 (243)
T 2q7f_A          135 LVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALE  214 (243)
T ss_dssp             HHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHH
Confidence            5566677777788888777665  777888899999999999999999887653  356688889999999999999999


Q ss_pred             HHHHHHhccccC
Q 040338          371 VMRNLLQLDVKV  382 (385)
Q Consensus       371 ~~~~~~~~~~~~  382 (385)
                      .++++.+..|.+
T Consensus       215 ~~~~~~~~~p~~  226 (243)
T 2q7f_A          215 MLDKAIDIQPDH  226 (243)
T ss_dssp             HHHHHHHHCTTC
T ss_pred             HHHHHHccCcch
Confidence            999998887764

>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=99.41  E-value=1.1e-11  Score=104.10  Aligned_cols=200  Identities=10%  Similarity=0.011  Sum_probs=150.9

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ...|..+...+..   .|++++|...++.+.+.. +.+...+..+...|...|++++|.+.|+++.+.+           
T Consensus        37 ~~~~~~~a~~~~~---~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-----------  101 (252)
T 2ho1_A           37 RDAYIQLGLGYLQ---RGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-----------  101 (252)
T ss_dssp             HHHHHHHHHHHHH---TTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHHHHHHHH---cCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-----------
Confidence            4556666666656   899999999999998874 4467888899999999999999999998876544           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                              +.+...+..+...+...|++++|.++|+++.+.+..| +...+..+...+...|++++|.+.++...+....
T Consensus       102 --------~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~  173 (252)
T 2ho1_A          102 --------SRNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRN  173 (252)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC
T ss_pred             --------cCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcc
Confidence                    3567788889999999999999999999998744455 4567778888899999999999999998887532


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHH
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRF  284 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~  284 (385)
                                             +...+..+...+...|++++|...++...+.   +...+..+...+           
T Consensus       174 -----------------------~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~-----------  219 (252)
T 2ho1_A          174 -----------------------QPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLA-----------  219 (252)
T ss_dssp             -----------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHH-----------
T ss_pred             -----------------------cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHH-----------
Confidence                                   2334566777788888999999999888652   333444444444           


Q ss_pred             HHHHHHHHHHhcccCChhhHHHHHHHHHhccc
Q 040338          285 FFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY  316 (385)
Q Consensus       285 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  316 (385)
                                 ...|+.++|.+.++.+.+..+
T Consensus       220 -----------~~~g~~~~A~~~~~~~~~~~p  240 (252)
T 2ho1_A          220 -----------KVFEDRDTAASYGLQLKRLYP  240 (252)
T ss_dssp             -----------HHTTCHHHHHHHHHHHHHHCT
T ss_pred             -----------HHccCHHHHHHHHHHHHHHCC
Confidence                       445556666666666665554

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.41  E-value=1.2e-11  Score=110.98  Aligned_cols=293  Identities=9%  Similarity=-0.049  Sum_probs=206.0

Q ss_pred             HHHHHHHHhhhccCChHHHHHHHHHHHHhc--cCCC--chHHHhHHHHHH--hcCChhHHH-----------HHHHhccC
Q 040338           53 NTMINGGVRCLCVGNIKMALHLHGLVKKFY--FVSD--ESIAKSSIDMHV--KCGAVDYAE-----------SAFLRMLN  115 (385)
Q Consensus        53 ~~li~~~~~~~~~~~~~~a~~~~~~m~~~g--~~~~--~~~~~~li~~~~--~~g~~~~a~-----------~~~~~m~~  115 (385)
                      ..+|.-+-.+.+.+++++|..+++++.+.-  ...|  ...|-.++..-.  -.+.++.+.           +.++.+..
T Consensus        13 ~~~l~~w~~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~   92 (383)
T 3ulq_A           13 GEKINEWYMYIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDK   92 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHh
Confidence            444554444555899999999999997752  2223  333444443221  123333333           44444322


Q ss_pred             CCccccccchHHHHHHhcCCCCCC----cchHHHHHHHHHhCCCchHHHHHHHHHHHC----CCCC-CHhhHHHHHHHhc
Q 040338          116 PSLFCWKFGIIRLLIMFQKMPERD----LVSWNTMISILTRHGFGFETLCTFIELWNH----GFGL-SSMLYATAFSARA  186 (385)
Q Consensus       116 ~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~  186 (385)
                      ...                  +.+    ...+......+...|++++|+..|++..+.    +-.+ ...++..+...+.
T Consensus        93 ~~~------------------~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~  154 (383)
T 3ulq_A           93 KQA------------------RLTGLLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYY  154 (383)
T ss_dssp             HTH------------------HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHH
T ss_pred             cCC------------------CchhHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHH
Confidence            110                  001    011222456678899999999999999764    2122 3467888889999


Q ss_pred             CccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----C
Q 040338          187 SVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----R  261 (385)
Q Consensus       187 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~  261 (385)
                      ..|+++.|...+++..+.....+..                ......+++.+...|...|++++|+..|++..+     +
T Consensus       155 ~~~~~~~A~~~~~~al~~~~~~~~~----------------~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~  218 (383)
T 3ulq_A          155 YMKQTYFSMDYARQAYEIYKEHEAY----------------NIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEK  218 (383)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHTCSTT----------------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCCHHHHHHHHHHHHHHHHhCccc----------------hHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999988752211110                011234567888889999999999999987764     1


Q ss_pred             C----hhhHHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc---
Q 040338          262 N----MISWMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY---  316 (385)
Q Consensus       262 ~----~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---  316 (385)
                      +    ..++..+...|...|++++|+..+                  ++..+...+...|++++|...+++..+...   
T Consensus       219 ~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~  298 (383)
T 3ulq_A          219 QPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAG  298 (383)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcC
Confidence            2    247888899999999999999888                  688889999999999999999998877532   


Q ss_pred             ----hhhHHHHHHHHHccCC---HHHHHHHHHhCCCCCC-cchHHHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          317 ----TCYFVCMVDLLGLSGL---LGEAKKLIDEMPSKPT-CVIWGALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       317 ----~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                          ...+..+...+...|+   +++|..++++....|+ ...+..+...|...|++++|...+++..+..
T Consensus       299 ~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~~~  369 (383)
T 3ulq_A          299 DVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQVR  369 (383)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                3336678888999999   9999999999865433 4467789999999999999999999987643

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.41  E-value=6e-11  Score=100.81  Aligned_cols=233  Identities=10%  Similarity=-0.020  Sum_probs=168.6

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC--cch
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD--LVS  142 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~--~~~  142 (385)
                      .|++++|...++...+.. +.+...+..+..+|...|++++|...|++..+...                  .++  ..+
T Consensus        16 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~------------------~~~~~~~~   76 (272)
T 3u4t_A           16 NNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVN------------------ATKAKSAD   76 (272)
T ss_dssp             TTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSC------------------TTTCCHHH
T ss_pred             hcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccC------------------chhHHHHH
Confidence            899999999999999864 33566889999999999999999999998876221                  232  234


Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHh
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLK  222 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  222 (385)
                      |..+...+...|++++|+..|++..+.. +.+..++..+...+...|++++|...++...+..+ .              
T Consensus        77 ~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-~--------------  140 (272)
T 3u4t_A           77 FEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTT-T--------------  140 (272)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSC-C--------------
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCC-C--------------
Confidence            8889999999999999999999998852 23567888999999999999999999999877632 1              


Q ss_pred             cCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCC---CCchHHHHHHHHHHHHhc
Q 040338          223 CGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGV---LEKPRFFFFFVSLLSGCS  296 (385)
Q Consensus       223 ~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~---~~~a~~~~~~~~l~~~~~  296 (385)
                              +...+..+...+...+++++|...|++..+  | +...+..+...+...|+   +++|+..+          
T Consensus       141 --------~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~----------  202 (272)
T 3u4t_A          141 --------DPKVFYELGQAYYYNKEYVKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYY----------  202 (272)
T ss_dssp             --------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHH----------
T ss_pred             --------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHH----------
Confidence                    223344555233334599999999998876  3 45666667777777776   66665543          


Q ss_pred             ccCChhhHHHHHHHHHhcc---chhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFT---YTCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGAL  355 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~l  355 (385)
                           +++.++........   ....+..+...|.+.|++++|.+.|++..+. |+ ...+..+
T Consensus       203 -----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l  261 (272)
T 3u4t_A          203 -----EKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILALDPTNKKAIDGL  261 (272)
T ss_dssp             -----HHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             -----HHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCccHHHHHHHh
Confidence                 22222222111110   1367777888999999999999999988752 44 3334433

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.41  E-value=2.2e-11  Score=100.12  Aligned_cols=202  Identities=8%  Similarity=-0.062  Sum_probs=159.7

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      .+...|..+...+...|++++|...|+++.+.. +.+...+..+...+...|++++|.+.++.+.+....          
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~----------   74 (225)
T 2vq2_A            6 QVSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPD----------   74 (225)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----------
T ss_pred             ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC----------
Confidence            356678889999999999999999999998752 335778888999999999999999999999887531          


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcC-CChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEG-GSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSG  294 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~-g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~  294 (385)
                                   +..++..+...+... |++++|...++++.+  .+.                .   ....+..+...
T Consensus        75 -------------~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~----------------~---~~~~~~~l~~~  122 (225)
T 2vq2_A           75 -------------SAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYP----------------T---PYIANLNKGIC  122 (225)
T ss_dssp             -------------CHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCS----------------C---HHHHHHHHHHH
T ss_pred             -------------ChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCc----------------c---hHHHHHHHHHH
Confidence                         234556777888888 999999999998876  111                0   01133445555


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C--CcchHHHHHHHHHhcCChHHHH
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P--TCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p--~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      +...|++++|...++++.+..+  ...+..+...+.+.|++++|.+.+++.... |  +...+..+...+...|+.+++.
T Consensus       123 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~  202 (225)
T 2vq2_A          123 SAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAY  202 (225)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHH
Confidence            6666777888888888877666  777888999999999999999999988663 4  5566777888889999999999


Q ss_pred             HHHHHHHhccccC
Q 040338          370 LVMRNLLQLDVKV  382 (385)
Q Consensus       370 ~~~~~~~~~~~~~  382 (385)
                      .+++.+.+..|..
T Consensus       203 ~~~~~~~~~~p~~  215 (225)
T 2vq2_A          203 EYEAQLQANFPYS  215 (225)
T ss_dssp             HHHHHHHHHCTTC
T ss_pred             HHHHHHHHhCCCC
Confidence            9999998877664

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.40  E-value=4e-12  Score=106.12  Aligned_cols=119  Identities=9%  Similarity=-0.005  Sum_probs=59.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...++++.+.. +.+...+..+...|...|++++|.+.|++..+.+                   +.+..++.
T Consensus        36 ~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~   95 (243)
T 2q7f_A           36 FGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-------------------SSAATAYY   95 (243)
T ss_dssp             ------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             hhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------------------CcchHHHH
Confidence            556666666665555532 2244555555555555566666665555544322                   23444555


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      .+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++.+.+.
T Consensus        96 ~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  154 (243)
T 2q7f_A           96 GAGNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL  154 (243)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            55555555566666666555555432 223444455555555555555555555555544

>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=99.40  E-value=4.1e-11  Score=106.92  Aligned_cols=243  Identities=9%  Similarity=0.027  Sum_probs=183.1

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC-hhHHHHHHHhccCCCccccccchHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA-VDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ..|+.+-..+..   .|++++|+..+++..+.. +-+...|+.+..++.+.|+ +++|+..|++..+.+           
T Consensus        98 ~a~~~lg~~~~~---~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-----------  162 (382)
T 2h6f_A           98 DVYDYFRAVLQR---DERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-----------  162 (382)
T ss_dssp             HHHHHHHHHHHH---TCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHHHHHHH---CCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-----------
Confidence            456666666555   899999999999999875 3367889999999999997 999999999987766           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                              +.+...|+.+..++...|++++|+..|+++.+.  .| +...|..+..++.+.|++++|+..++.+++..+.
T Consensus       163 --------P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~  232 (382)
T 2h6f_A          163 --------PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR  232 (382)
T ss_dssp             --------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT
T ss_pred             --------CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC
Confidence                    467889999999999999999999999999985  44 6788999999999999999999999999998642


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc-CCChhHH-----HHHHHhccc--C-ChhhHHHHHHHHHhcCC
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE-GGSTQKA-----DLAFELMSR--R-NMISWMVLISAFSQAGV  278 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~-~g~~~~A-----~~~~~~m~~--~-~~~~~~~li~~~~~~g~  278 (385)
                                             +...|+.+...+.+ .|..++|     +..|++..+  | +...|+.+...+...|.
T Consensus       233 -----------------------~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~  289 (382)
T 2h6f_A          233 -----------------------NNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGL  289 (382)
T ss_dssp             -----------------------CHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCG
T ss_pred             -----------------------CHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCc
Confidence                                   33455666666666 5555777     467776654  3 45566666666655441


Q ss_pred             CCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC---------CHHHHHHHHHhC-CC-
Q 040338          279 LEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG---------LLGEAKKLIDEM-PS-  345 (385)
Q Consensus       279 ~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g---------~~~~A~~~~~~m-~~-  345 (385)
                                          ++.++|...+.++ +..+  ...+..+...|.+.|         ..++|+++|+++ .+ 
T Consensus       290 --------------------~~~~~a~~~~~~~-~~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l~~~~  348 (382)
T 2h6f_A          290 --------------------SKYPNLLNQLLDL-QPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEK  348 (382)
T ss_dssp             --------------------GGCHHHHHHHHHH-TTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHTT
T ss_pred             --------------------cchHHHHHHHHHh-ccCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHh
Confidence                                1355666666666 4444  677778888888764         258899999998 44 


Q ss_pred             CCCc-chHHHHHHHHHh
Q 040338          346 KPTC-VIWGALLGACCS  361 (385)
Q Consensus       346 ~p~~-~~~~~li~~~~~  361 (385)
                      .|.. ..|..+...+..
T Consensus       349 DP~r~~~w~~~~~~l~~  365 (382)
T 2h6f_A          349 DTIRKEYWRYIGRSLQS  365 (382)
T ss_dssp             CGGGHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHH
Confidence            3543 356666665544

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.39  E-value=6e-12  Score=110.12  Aligned_cols=249  Identities=10%  Similarity=-0.053  Sum_probs=188.7

Q ss_pred             ccCChHHHHHHHHHHHHhccCCC----chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC--
Q 040338           64 CVGNIKMALHLHGLVKKFYFVSD----ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE--  137 (385)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~--  137 (385)
                      ..|++++|...++++.+.... +    ...+..+...|...|++++|.+.+++..+.               ......  
T Consensus        17 ~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---------------~~~~~~~~   80 (338)
T 3ro2_A           17 KSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTL---------------ARTIGDQL   80 (338)
T ss_dssp             HTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------HHHHTCHH
T ss_pred             HhccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---------------hhcccccH
Confidence            389999999999999987422 3    367888999999999999999999775321               111111  


Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCC-CCC----HhhHHHHHHHhcCccC--------------------cc
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGF-GLS----SMLYATAFSARASVYD--------------------LE  192 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~----~~t~~~ll~~~~~~~~--------------------~~  192 (385)
                      ....++..+...+...|++++|...+++..+... .++    ..++..+...+...|+                    ++
T Consensus        81 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  160 (338)
T 3ro2_A           81 GEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQ  160 (338)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHH
Confidence            2355788888999999999999999998765311 112    3477788888899999                    88


Q ss_pred             chhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----CC----h
Q 040338          193 WGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----RN----M  263 (385)
Q Consensus       193 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~~----~  263 (385)
                      +|.+.+++......               +.+  +......++..+...+...|++++|...+++..+     ++    .
T Consensus       161 ~A~~~~~~a~~~~~---------------~~~--~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  223 (338)
T 3ro2_A          161 AAVDLYEENLSLVT---------------ALG--DRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAER  223 (338)
T ss_dssp             HHHHHHHHHHHHHH---------------HHT--CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHH---------------hcC--CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHH
Confidence            88888877654311               000  0011234567778888889999999999988764     12    2


Q ss_pred             hhHHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------h
Q 040338          264 ISWMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------T  317 (385)
Q Consensus       264 ~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~  317 (385)
                      .++..+...+...|++++|+..+                  ++..+...+...|++++|...+++......        .
T Consensus       224 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  303 (338)
T 3ro2_A          224 RAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEG  303 (338)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHH
Confidence            37788888999999999999888                  677888889999999999999998876543        4


Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ..+..+...|.+.|++++|.+.+++..+
T Consensus       304 ~~~~~la~~~~~~g~~~~A~~~~~~a~~  331 (338)
T 3ro2_A          304 RACWSLGNAYTALGNHDQAMHFAEKHLE  331 (338)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            4777899999999999999999987653

>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=99.39  E-value=6.1e-11  Score=101.09  Aligned_cols=225  Identities=5%  Similarity=-0.088  Sum_probs=154.0

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHh----cCChhHHHHHHHhccCCCcccccc
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVK----CGAVDYAESAFLRMLNPSLFCWKF  123 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~  123 (385)
                      ++.++..+-..+..   .|++++|...|++..+   +.+...+..+...|..    .+++++|.+.|++..+.       
T Consensus         5 ~~~a~~~lg~~~~~---~~~~~~A~~~~~~a~~---~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~-------   71 (273)
T 1ouv_A            5 DPKELVGLGAKSYK---EKDFTQAKKYFEKACD---LKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDL-------   71 (273)
T ss_dssp             CHHHHHHHHHHHHH---TTCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT-------
T ss_pred             ChHHHHHHHHHHHh---CCCHHHHHHHHHHHHH---CCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHC-------
Confidence            44455555555545   6788888888887776   6666777777777777    78888888887765432       


Q ss_pred             chHHHHHHhcCCCCCCcchHHHHHHHHHh----CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC----ccCccchh
Q 040338          124 GIIRLLIMFQKMPERDLVSWNTMISILTR----HGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS----VYDLEWGP  195 (385)
Q Consensus       124 ~~~~a~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~  195 (385)
                                    .+...+..+...|..    .+++++|+..|++..+.+   +...+..+...+..    .+++++|.
T Consensus        72 --------------~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~  134 (273)
T 1ouv_A           72 --------------NYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAV  134 (273)
T ss_dssp             --------------TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             --------------CCHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHH
Confidence                          245667777777777    788888888888877764   55666677777776    77888888


Q ss_pred             hHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc----CCChhHHHHHHHhcccC-ChhhHHHHH
Q 040338          196 HLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE----GGSTQKADLAFELMSRR-NMISWMVLI  270 (385)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~-~~~~~~~li  270 (385)
                      ..++...+.+                         +...+..+...|..    .+++++|+..|++..+. +...+..+.
T Consensus       135 ~~~~~a~~~~-------------------------~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg  189 (273)
T 1ouv_A          135 EYFTKACDLN-------------------------DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAG  189 (273)
T ss_dssp             HHHHHHHHTT-------------------------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHhcC-------------------------cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            8887776654                         22456667777776    77888888888776543 333343444


Q ss_pred             HHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCC
Q 040338          271 SAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPS  345 (385)
Q Consensus       271 ~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~  345 (385)
                      ..|...                  ....+++++|...+++..+.+....+..+...|.+    .+++++|.+.|++..+
T Consensus       190 ~~~~~g------------------~~~~~~~~~A~~~~~~a~~~~~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~  250 (273)
T 1ouv_A          190 NMYHHG------------------EGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCK  250 (273)
T ss_dssp             HHHHHT------------------CSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHH
T ss_pred             HHHHcC------------------CCCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHH
Confidence            333330                  01167777788888887777776677777778877    8888888888876554

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.38  E-value=1.4e-10  Score=106.96  Aligned_cols=282  Identities=11%  Similarity=-0.013  Sum_probs=195.2

Q ss_pred             CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCC-----CCCCcchHHHHHHHHHhCCCchH
Q 040338           84 VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKM-----PERDLVSWNTMISILTRHGFGFE  158 (385)
Q Consensus        84 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~-----~~~~~~~~~~li~~~~~~~~~~~  158 (385)
                      ......||.|...+...|+.++|++.|++..               +++.+.     .+....+|+.+..+|...|++++
T Consensus        48 ~~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl---------------~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~  112 (472)
T 4g1t_A           48 EFKATMCNLLAYLKHLKGQNEAALECLRKAE---------------ELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSD  112 (472)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------HHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHH
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------HHHHhcCccccchHHHHHHHHHHHHHHHcCChHH
Confidence            3446789999999999999999999997642               222211     12345689999999999999999


Q ss_pred             HHHHHHHHHHC-----C-CCC-CHhhHHHHHHHhcC--ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc---CCC
Q 040338          159 TLCTFIELWNH-----G-FGL-SSMLYATAFSARAS--VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC---GCN  226 (385)
Q Consensus       159 a~~~~~~m~~~-----g-~~p-~~~t~~~ll~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~---g~~  226 (385)
                      |...+++..+.     + ..+ ...++.....++..  .+++++|+..|++.++..+. ++..+..+..++.+.   ++.
T Consensus       113 A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~~l~~~~~~  191 (472)
T 4g1t_A          113 VQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASYRLDNWPPS  191 (472)
T ss_dssp             HHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCchHH
Confidence            99999887642     1 112 24456555444443  45789999999999987642 444555555554443   333


Q ss_pred             C------------CCchhhHHHHHHHHHHc----CCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH-
Q 040338          227 G------------IESSIQIGKALVTMYAE----GGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF-  286 (385)
Q Consensus       227 ~------------~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~-  286 (385)
                      +            .+.+..++..+...+..    .|+.++|...+++..+   .+...+..+...|...|++++|+..+ 
T Consensus       192 ~~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~  271 (472)
T 4g1t_A          192 QNAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLK  271 (472)
T ss_dssp             CCTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHH
Confidence            3            33445566666555554    4678899999987754   35678888999999999999999988 


Q ss_pred             -----------HHHHHHHHhcc-------------------cCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHH
Q 040338          287 -----------FFVSLLSGCSH-------------------SGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLG  334 (385)
Q Consensus       287 -----------~~~~l~~~~~~-------------------~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~  334 (385)
                                 ++..+...|..                   .+..+.|...+++.....+  ...+..+...|...|+++
T Consensus       272 ~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~  351 (472)
T 4g1t_A          272 KALEYIPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYE  351 (472)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHH
T ss_pred             HHHHhCCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHH
Confidence                       44444444422                   2335677888888777766  788888999999999999


Q ss_pred             HHHHHHHhCCCC-CCcc----hHHHHHH-HHHhcCChHHHHHHHHHHHhcccc
Q 040338          335 EAKKLIDEMPSK-PTCV----IWGALLG-ACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       335 ~A~~~~~~m~~~-p~~~----~~~~li~-~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      +|++.|++..+. |+..    .+..+.. .+...|++++|+..+++.++.++.
T Consensus       352 ~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~  404 (472)
T 4g1t_A          352 EAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQK  404 (472)
T ss_dssp             HHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcc
Confidence            999999987643 3322    2333332 345678999999999998887664

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.38  E-value=4.5e-11  Score=98.31  Aligned_cols=167  Identities=13%  Similarity=-0.051  Sum_probs=131.3

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      +...|..+...+..   .|++++|.+.++.+.+.. +.+...+..+...|...|++++|.+.|++..+.+          
T Consensus         7 ~~~~~~~~~~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~----------   72 (225)
T 2vq2_A            7 VSNIKTQLAMEYMR---GQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK----------   72 (225)
T ss_dssp             HHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             cHHHHHHHHHHHHH---HhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC----------
Confidence            34566677777666   899999999999998864 3467788889999999999999999998876544          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhC-CCchHHHHHHHHHHHCCCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRH-GFGFETLCTFIELWNHGFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                               +.+..++..+...+... |++++|...++++.+.+..|+ ...+..+..++...|++++|...++.+.+..
T Consensus        73 ---------~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  143 (225)
T 2vq2_A           73 ---------PDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ  143 (225)
T ss_dssp             ---------TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             ---------CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence                     35667888889999999 999999999999987433443 5677788888999999999999999988764


Q ss_pred             CCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          206 PSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       206 ~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                      +.                       +...+..+...+.+.|++++|...++...+
T Consensus       144 ~~-----------------------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  175 (225)
T 2vq2_A          144 PQ-----------------------FPPAFKELARTKMLAGQLGDADYYFKKYQS  175 (225)
T ss_dssp             TT-----------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CC-----------------------CchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            32                       233456667777778899999999988764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.33  E-value=1.2e-11  Score=98.86  Aligned_cols=152  Identities=12%  Similarity=-0.004  Sum_probs=136.6

Q ss_pred             hhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHh
Q 040338          231 SIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGC  295 (385)
Q Consensus       231 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~  295 (385)
                      +..+|..+...|.+.|++++|+..|++..+  | +..++..+..+|.+.|++++|+..+            .+..+...+
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~   83 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSAN   83 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHH
Confidence            567788999999999999999999998875  4 6788999999999999999999988            777888888


Q ss_pred             cccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELV  371 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~  371 (385)
                      ...++++.+...+.+.....+  ...+..+...|.+.|++++|++.|++..+ .| +..+|..+..+|.+.|++++|++.
T Consensus        84 ~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~  163 (184)
T 3vtx_A           84 FMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKY  163 (184)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHH
Confidence            999999999999999988877  78888899999999999999999998876 34 567899999999999999999999


Q ss_pred             HHHHHhccccC
Q 040338          372 MRNLLQLDVKV  382 (385)
Q Consensus       372 ~~~~~~~~~~~  382 (385)
                      |++.++.+|+.
T Consensus       164 ~~~al~~~p~~  174 (184)
T 3vtx_A          164 FKKALEKEEKK  174 (184)
T ss_dssp             HHHHHHTTHHH
T ss_pred             HHHHHhCCccC
Confidence            99999988764

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.33  E-value=2.1e-11  Score=105.69  Aligned_cols=255  Identities=7%  Similarity=-0.064  Sum_probs=160.8

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCC----CCCCcchHHHHHHHHHhCCCchHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKM----PERDLVSWNTMISILTRHGFGFETLC  161 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~li~~~~~~~~~~~a~~  161 (385)
                      +..++..+...|...|++++|..+|+++.+.               +...    .+....++..+...|...|++++|..
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~---------------~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~   90 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALED---------------LEKTSGHDHPDVATMLNILALVYRDQNKYKDAAN   90 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------HHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---------------HHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            3566778888888889999999888776431               1111    02345678889999999999999999


Q ss_pred             HHHHHHHC------CCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhH
Q 040338          162 TFIELWNH------GFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQI  234 (385)
Q Consensus       162 ~~~~m~~~------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~  234 (385)
                      .+++..+.      +-.| ...++..+...+...|++++|...+++..+....               ....+.+....+
T Consensus        91 ~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~---------------~~~~~~~~~~~~  155 (311)
T 3nf1_A           91 LLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREK---------------VLGKDHPDVAKQ  155 (311)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH---------------HHCTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHH---------------hcCCCChHHHHH
Confidence            99998764      2233 4567888999999999999999999998875200               000001123345


Q ss_pred             HHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhc
Q 040338          235 GKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKF  314 (385)
Q Consensus       235 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  314 (385)
                      +..+...+...|++++|+..|++..+.           +.+....+......++..+...+...|++++|...++++.+.
T Consensus       156 ~~~la~~~~~~~~~~~A~~~~~~a~~~-----------~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  224 (311)
T 3nf1_A          156 LNNLALLCQNQGKYEEVEYYYQRALEI-----------YQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTR  224 (311)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHH-----------HHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH-----------HHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            678888899999999999999887541           011100011111114445555556666666666666666543


Q ss_pred             cc-----------------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          315 TY-----------------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       315 ~~-----------------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      ..                 ...+..+...+...+.+.+|...++.....  .+..+|..+...|.+.|++++|...+++.
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  304 (311)
T 3nf1_A          225 AHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAA  304 (311)
T ss_dssp             HHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            21                 222333344445566666666777666653  34567889999999999999999999999


Q ss_pred             Hhcccc
Q 040338          376 LQLDVK  381 (385)
Q Consensus       376 ~~~~~~  381 (385)
                      .+..+.
T Consensus       305 l~l~~~  310 (311)
T 3nf1_A          305 MRSRKQ  310 (311)
T ss_dssp             HHHHC-
T ss_pred             HHHhhc
Confidence            876553

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.32  E-value=8.2e-11  Score=105.57  Aligned_cols=219  Identities=6%  Similarity=-0.086  Sum_probs=167.8

Q ss_pred             HHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC--CcchHHHHHHHHHhCCCchHHHHHHHHHHHCC
Q 040338           93 SIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER--DLVSWNTMISILTRHGFGFETLCTFIELWNHG  170 (385)
Q Consensus        93 li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  170 (385)
                      ....+...|++++|...|++..+.               +...+.+  ...+|..+...|...|++++|+..+++..+.-
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~---------------~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~  173 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESK---------------LIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIY  173 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTT---------------GGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHH---------------HhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            556777899999999999876543               2222111  34678889999999999999999999986531


Q ss_pred             --C---CC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC-CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHH
Q 040338          171 --F---GL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS-LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA  243 (385)
Q Consensus       171 --~---~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~  243 (385)
                        .   .| ...++..+...+...|++++|...++...+.... ++..                  ....++..+...|.
T Consensus       174 ~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~------------------~~~~~~~~lg~~y~  235 (383)
T 3ulq_A          174 KEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQ------------------LMGRTLYNIGLCKN  235 (383)
T ss_dssp             HTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH------------------HHHHHHHHHHHHHH
T ss_pred             HhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChH------------------HHHHHHHHHHHHHH
Confidence              1   11 2457788889999999999999999998865221 1111                  12245678888999


Q ss_pred             cCCChhHHHHHHHhccc-----CC----hhhHHHHHHHHHhcCCCCchHHHH-----------------HHHHHHHHhcc
Q 040338          244 EGGSTQKADLAFELMSR-----RN----MISWMVLISAFSQAGVLEKPRFFF-----------------FFVSLLSGCSH  297 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~-----------------~~~~l~~~~~~  297 (385)
                      ..|++++|+..|++..+     .+    ..++..+...|.+.|++++|...+                 .+..+...+..
T Consensus       236 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~  315 (383)
T 3ulq_A          236 SQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLS  315 (383)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTS
T ss_pred             HCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhC
Confidence            99999999999988765     22    356888899999999999999988                 45678888888


Q ss_pred             cCC---hhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          298 SGP---VTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       298 ~~~---~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      .|+   .++|..++++...... ...+..+...|...|++++|.+.+++..
T Consensus       316 ~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          316 GPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            998   8888888887744333 6778889999999999999999998764

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.31  E-value=3.6e-11  Score=104.12  Aligned_cols=257  Identities=11%  Similarity=-0.026  Sum_probs=165.5

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh-------ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCcccc
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF-------YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCW  121 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-------g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~  121 (385)
                      ..++..+...+..   .|++++|..+++++.+.       ..+....++..+...|...|++++|...+++..+      
T Consensus        27 ~~~~~~l~~~~~~---~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~------   97 (311)
T 3nf1_A           27 LRTLHNLVIQYAS---QGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALA------   97 (311)
T ss_dssp             HHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH------
T ss_pred             HHHHHHHHHHHHH---cCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH------
Confidence            3456667777666   89999999999999874       2333567788899999999999999999977643      


Q ss_pred             ccchHHHHHHhcCC----CCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC------CCCC-CHhhHHHHHHHhcCccC
Q 040338          122 KFGIIRLLIMFQKM----PERDLVSWNTMISILTRHGFGFETLCTFIELWNH------GFGL-SSMLYATAFSARASVYD  190 (385)
Q Consensus       122 ~~~~~~a~~~~~~~----~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p-~~~t~~~ll~~~~~~~~  190 (385)
                               ++.+.    .+....++..+...|...|++++|...|++..+.      +-.| ....+..+...+...|+
T Consensus        98 ---------~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~  168 (311)
T 3nf1_A           98 ---------IREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGK  168 (311)
T ss_dssp             ---------HHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTC
T ss_pred             ---------HHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCC
Confidence                     22111    1234567888999999999999999999998764      2334 45667888899999999


Q ss_pred             ccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHH
Q 040338          191 LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLI  270 (385)
Q Consensus       191 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li  270 (385)
                      +++|.+.++...+...               +....+.+....++..+...|...|++++|...+++..+.....     
T Consensus       169 ~~~A~~~~~~a~~~~~---------------~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~-----  228 (311)
T 3nf1_A          169 YEEVEYYYQRALEIYQ---------------TKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHER-----  228 (311)
T ss_dssp             HHHHHHHHHHHHHHHH---------------HTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH-----
T ss_pred             HHHHHHHHHHHHHHHH---------------HHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-----
Confidence            9999999999887510               00000011123456778888889999999999999887411000     


Q ss_pred             HHHHhcCCCCchHHHH--HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          271 SAFSQAGVLEKPRFFF--FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       271 ~~~~~~g~~~~a~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                       .+.............  .+..+...+...+.+.++...++......+  ..++..+...|.+.|++++|.+.|++..
T Consensus       229 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  305 (311)
T 3nf1_A          229 -EFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAM  305 (311)
T ss_dssp             -HHC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             -cCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence             000000000000000  333344444556666777777777766555  7778888888889999999988887654

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.31  E-value=2.8e-10  Score=104.37  Aligned_cols=287  Identities=10%  Similarity=-0.032  Sum_probs=182.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCCh---hHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcc
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAV---DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLV  141 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~---~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~  141 (385)
                      .|++++|.++|+...+.|   +...+..|...|...|+.   ++|...|++..+                      .+..
T Consensus        16 ~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~----------------------~~~~   70 (452)
T 3e4b_A           16 RGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAAD----------------------TSPR   70 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHT---CCTGGGTCC--------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHh----------------------CCHH
Confidence            688999999999888775   445555666677777777   788888866543                      2445


Q ss_pred             hHHHHHHHHHhCC-----CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          142 SWNTMISILTRHG-----FGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       142 ~~~~li~~~~~~~-----~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      .+..|...+...+     ++++|+.+|++..+.|...   .+..|...|...+..+.+.+.++.+.+.....+......|
T Consensus        71 A~~~Lg~~~~~~~~~~~~~~~~A~~~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~L  147 (452)
T 3e4b_A           71 AQARLGRLLAAKPGATEAEHHEAESLLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQ  147 (452)
T ss_dssp             CHHHHHHHHHTC--CCHHHHHHHHHHHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHH
Confidence            5666666454544     6778888888888765433   4555555555555544444444443332111123344445


Q ss_pred             HHHHHhcCCCC-------------CCchhhHHHHHHHHHHcCC---ChhHHHHHHHhcccC---ChhhHHHHHHHHHhc-
Q 040338          217 IDMYLKCGCNG-------------IESSIQIGKALVTMYAEGG---STQKADLAFELMSRR---NMISWMVLISAFSQA-  276 (385)
Q Consensus       217 i~~~~~~g~~~-------------~~~~~~~~~~li~~~~~~g---~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~-  276 (385)
                      ...|...+..+             ...+...+..|...|.+.|   +.++|+..|++..+.   +...+..|...|... 
T Consensus       148 g~~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~  227 (452)
T 3e4b_A          148 VLLYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDAT  227 (452)
T ss_dssp             HHHHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGG
T ss_pred             HHHHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence            55555544332             2233447888889999999   899999999888653   334446677777554 


Q ss_pred             ---CCCCchHHHH---------HHHHHHHH-h--cccCChhhHHHHHHHHHhccchhhHHHHHHHHHccC-----CHHHH
Q 040338          277 ---GVLEKPRFFF---------FFVSLLSG-C--SHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGLSG-----LLGEA  336 (385)
Q Consensus       277 ---g~~~~a~~~~---------~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~~g-----~~~~A  336 (385)
                         +++++|+..|         .+..+... +  ...++.++|...|++..+.+.......|...|. .|     ++++|
T Consensus       228 ~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G~g~~~d~~~A  306 (452)
T 3e4b_A          228 LGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-EGKWVPADAKAA  306 (452)
T ss_dssp             GSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HCSSSCCCHHHH
T ss_pred             CCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cCCCCCCCHHHH
Confidence               5777888887         45555554 3  458999999999999999888777777888887 55     99999


Q ss_pred             HHHHHhCCCCCCcchHHHHHHHHHh----cCChHHHHHHHHHHHhcccc
Q 040338          337 KKLIDEMPSKPTCVIWGALLGACCS----HYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       337 ~~~~~~m~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~  381 (385)
                      .+.|++.. ..+...+..|...|..    ..+.++|..+|++..+.|..
T Consensus       307 ~~~~~~Aa-~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~  354 (452)
T 3e4b_A          307 EAHFEKAV-GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQN  354 (452)
T ss_dssp             HHHHHTTT-TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCT
T ss_pred             HHHHHHHh-CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChH
Confidence            99999999 6677788888888877    34999999999999887654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.26  E-value=6.5e-10  Score=96.57  Aligned_cols=219  Identities=12%  Similarity=0.031  Sum_probs=162.2

Q ss_pred             hHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHH-------hCCCc-------hHHHHHHHHHHHC
Q 040338          104 DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILT-------RHGFG-------FETLCTFIELWNH  169 (385)
Q Consensus       104 ~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~-------~~~~~-------~~a~~~~~~m~~~  169 (385)
                      ++|..+|++....+                   +.+...|..+...+.       +.|++       ++|..+|++..+.
T Consensus        33 ~~a~~~~~~al~~~-------------------p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~   93 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-------------------GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST   93 (308)
T ss_dssp             HHHHHHHHHHHHHH-------------------TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHc-------------------CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH
Confidence            56667777665543                   467778888887775       45886       8999999999873


Q ss_pred             CCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCCh
Q 040338          170 GFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGST  248 (385)
Q Consensus       170 g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~  248 (385)
                       +.| +...|..+...+.+.|++++|.++|++.++..  |+..                    ..+|..+...+.+.|++
T Consensus        94 -~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~--------------------~~~~~~~~~~~~~~~~~  150 (308)
T 2ond_A           94 -LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE--DIDP--------------------TLVYIQYMKFARRAEGI  150 (308)
T ss_dssp             -TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSS--SSCT--------------------HHHHHHHHHHHHHHHCH
T ss_pred             -hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc--ccCc--------------------cHHHHHHHHHHHHhcCH
Confidence             355 45678888889999999999999999998853  2211                    01456666677777899


Q ss_pred             hHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHH-hcccCChhhHHHHHHHHHhccc--hhhHHHHHH
Q 040338          249 QKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSG-CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVD  325 (385)
Q Consensus       249 ~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~  325 (385)
                      ++|..+|++..+.+...+...+                   ..... +...|+.++|..+|++..+..+  ...+..++.
T Consensus       151 ~~A~~~~~~a~~~~p~~~~~~~-------------------~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~  211 (308)
T 2ond_A          151 KSGRMIFKKAREDARTRHHVYV-------------------TAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYID  211 (308)
T ss_dssp             HHHHHHHHHHHTSTTCCTHHHH-------------------HHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHH-------------------HHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHH
Confidence            9999999998763221111111                   00111 1135888899999999888777  788888999


Q ss_pred             HHHccCCHHHHHHHHHhCCCC----C--CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          326 LLGLSGLLGEAKKLIDEMPSK----P--TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       326 ~~~~~g~~~~A~~~~~~m~~~----p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .+.+.|++++|..+|++....    |  ....|..++..+.+.|+.+.|..+++++.+..|...
T Consensus       212 ~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~~p~~~  275 (308)
T 2ond_A          212 YLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREEY  275 (308)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTT
T ss_pred             HHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccccc
Confidence            999999999999999988762    3  244788889999999999999999999998887643

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.23  E-value=7.1e-10  Score=88.30  Aligned_cols=169  Identities=9%  Similarity=-0.030  Sum_probs=136.5

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      ++..|..+-..+..   .|++++|++.|++..+.. +-+..++..+..+|.+.|++++|...+.......          
T Consensus         4 ~~~iy~~lG~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~----------   69 (184)
T 3vtx_A            4 TTTIYMDIGDKKRT---KGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD----------   69 (184)
T ss_dssp             CHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             HHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----------
Confidence            45677777777666   899999999999999875 3467889999999999999999999998875544          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                               +.+...+..+...+...++++.+...+.+.... .+-+...+..+...+.+.|++++|++.+++..+..+ 
T Consensus        70 ---------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~-~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p-  138 (184)
T 3vtx_A           70 ---------TTSAEAYYILGSANFMIDEKQAAIDALQRAIAL-NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKP-  138 (184)
T ss_dssp             ---------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             ---------chhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcc-
Confidence                     355667788888889999999999999998775 233567788888899999999999999999988753 


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCCh
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNM  263 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~  263 (385)
                                            .+..+|..+...|.+.|++++|+..|++..+.+.
T Consensus       139 ----------------------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  172 (184)
T 3vtx_A          139 ----------------------GFIRAYQSIGLAYEGKGLRDEAVKYFKKALEKEE  172 (184)
T ss_dssp             ----------------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTH
T ss_pred             ----------------------hhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhCCc
Confidence                                  2344567778888888899999999998876443

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.22  E-value=2.2e-10  Score=105.68  Aligned_cols=212  Identities=11%  Similarity=-0.038  Sum_probs=165.3

Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCCh-hHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAV-DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      ..++++...++...... +.+...+..+...|...|++ ++|++.|++..+.+                   +.+...|.
T Consensus        82 ~~~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-------------------p~~~~a~~  141 (474)
T 4abn_A           82 EEMEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-------------------PELVEAWN  141 (474)
T ss_dssp             HHHHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-------------------CCCHHHHH
Confidence            45677777777766542 34778889999999999999 99999998876655                   35678999


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCc---------cCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASV---------YDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                      .+..+|.+.|++++|...|++..+.  .|+...+..+...+...         |++++|++.+++.++..+. +.     
T Consensus       142 ~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~-----  213 (474)
T 4abn_A          142 QLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVL-DG-----  213 (474)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTT-CH-----
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCC-CH-----
Confidence            9999999999999999999999885  57778888999999999         9999999999999987532 23     


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcC--------CChhHHHHHHHhccc--C----ChhhHHHHHHHHHhcCCCCc
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEG--------GSTQKADLAFELMSR--R----NMISWMVLISAFSQAGVLEK  281 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~--------g~~~~A~~~~~~m~~--~----~~~~~~~li~~~~~~g~~~~  281 (385)
                                       ..|..+...|...        |++++|+..|++..+  |    +...|.              
T Consensus       214 -----------------~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~--------------  262 (474)
T 4abn_A          214 -----------------RSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHL--------------  262 (474)
T ss_dssp             -----------------HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHH--------------
T ss_pred             -----------------HHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHH--------------
Confidence                             3445555666665        789999999988865  2    233343              


Q ss_pred             hHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          282 PRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       282 a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                              .+..+|...|++++|...|++..+..+  ...+..+...+...|++++|.+.+..+.
T Consensus       263 --------~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~~~  319 (474)
T 4abn_A          263 --------NRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESKGKTK  319 (474)
T ss_dssp             --------HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTTCC
T ss_pred             --------HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence                    444455556667777788888777766  6677888888888999999988776664

>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=99.22  E-value=2.2e-08  Score=95.49  Aligned_cols=355  Identities=11%  Similarity=0.057  Sum_probs=223.2

Q ss_pred             ccCCChHHHHHHHHHHHHccc-chhhHHh---------h---hhhHHHHHhhhC--C---CChhhHHHHHHHHHhhhcc-
Q 040338            5 GSLKSLPIARKIHAQLISTCL-ISSIFLQ---------L---IDDDYRVFCDIG--P---RYLFTYNTMINGGVRCLCV-   65 (385)
Q Consensus         5 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~~---------~---~~~A~~~~~~~~--~---~~~~~~~~li~~~~~~~~~-   65 (385)
                      .+.+.++.++.++++++..-. .+..+..         +   ++.+..+|++..  .   |++..|...+.-..++... 
T Consensus        77 ~~~~~~~~aR~vyEraL~~fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~~  156 (679)
T 4e6h_A           77 VSLKQWKQVYETFDKLHDRFPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLWLSYITYVRKKNDII  156 (679)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHHHHHHHHHHHHSCST
T ss_pred             HhcCcHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhcccc
Confidence            345789999999999998742 3333332         5   899999999765  3   7787888777654442110 


Q ss_pred             ----CChHHHHHHHHHHHHh-cc-CCC-chHHHhHHHHHH---------hcCChhHHHHHHHhccCCCc----cccc---
Q 040338           66 ----GNIKMALHLHGLVKKF-YF-VSD-ESIAKSSIDMHV---------KCGAVDYAESAFLRMLNPSL----FCWK---  122 (385)
Q Consensus        66 ----~~~~~a~~~~~~m~~~-g~-~~~-~~~~~~li~~~~---------~~g~~~~a~~~~~~m~~~~~----~~~~---  122 (385)
                          +..+...++|+..... |. .|+ ...|...+....         ..++++.+.++|++......    ..|.   
T Consensus       157 ~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~  236 (679)
T 4e6h_A          157 TGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLCQPMDCLESMWQRYT  236 (679)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTTSCCSSHHHHHHHHH
T ss_pred             cccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence                1124455788776654 66 554 467777776654         23457788899988875321    1111   


Q ss_pred             -------------------cchHHHHHHhcC-------C----CC----------C--C------cchHHHHHHHHHhCC
Q 040338          123 -------------------FGIIRLLIMFQK-------M----PE----------R--D------LVSWNTMISILTRHG  154 (385)
Q Consensus       123 -------------------~~~~~a~~~~~~-------~----~~----------~--~------~~~~~~li~~~~~~~  154 (385)
                                         ..++.|...+.+       +    +.          |  +      ...|...+..--..+
T Consensus       237 ~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~  316 (679)
T 4e6h_A          237 QWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQQLLIWLEWIRWESDNK  316 (679)
T ss_dssp             HHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHHHHHHHHHHHHHHHhCC
Confidence                               111122222211       1    00          0  0      123444443322222


Q ss_pred             C-------chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchh-hHHHHHHHhCCCCchHHHHHHHHHHHhcCCC
Q 040338          155 F-------GFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGP-HLHSRVVHMEPSLDVFVGSGLIDMYLKCGCN  226 (385)
Q Consensus       155 ~-------~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  226 (385)
                      .       .+.+..+|++.... ++-+...|...+..+.+.|+.++|. ++++......+                    
T Consensus       317 ~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~P--------------------  375 (679)
T 4e6h_A          317 LELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCIP--------------------  375 (679)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHCT--------------------
T ss_pred             ccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCC--------------------
Confidence            0       12344556666553 2224455555555555667777775 77777765432                    


Q ss_pred             CCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-------------CC------------hhhHHHHHHHHHhcCCCCc
Q 040338          227 GIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-------------RN------------MISWMVLISAFSQAGVLEK  281 (385)
Q Consensus       227 ~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------------~~------------~~~~~~li~~~~~~g~~~~  281 (385)
                         .+...|-..+...-+.|+++.|.++|+.+.+             |+            ...|...+....+.|..+.
T Consensus       376 ---~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~  452 (679)
T 4e6h_A          376 ---NSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAA  452 (679)
T ss_dssp             ---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH
T ss_pred             ---CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHH
Confidence               2233445566666677888889988887764             21            1246666666677788888


Q ss_pred             hHHHH-------------HHHHHHHHhcc-cCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          282 PRFFF-------------FFVSLLSGCSH-SGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       282 a~~~~-------------~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      |..+|             .|......-.+ .++.+.|..+|+...+..+  ...+..+++.....|+.+.|..+|++...
T Consensus       453 AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~  532 (679)
T 4e6h_A          453 SRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVKSLFESSID  532 (679)
T ss_dssp             HHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            88877             22221111222 3568999999999888776  66777888888899999999999999887


Q ss_pred             C-C----CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          346 K-P----TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       346 ~-p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      . |    ....|...+..-.+.|+.+.+..+.+++.+..|++.
T Consensus       533 ~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~  575 (679)
T 4e6h_A          533 KISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVN  575 (679)
T ss_dssp             TSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCC
T ss_pred             hcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCc
Confidence            5 4    235788899999999999999999999999888753

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.22  E-value=6.8e-10  Score=99.36  Aligned_cols=290  Identities=11%  Similarity=-0.006  Sum_probs=199.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHHHHHhc--cCCC--chHHHhHHHHHH--hcCChhHHH---------HHHHhccCCCc
Q 040338           54 TMINGGVRCLCVGNIKMALHLHGLVKKFY--FVSD--ESIAKSSIDMHV--KCGAVDYAE---------SAFLRMLNPSL  118 (385)
Q Consensus        54 ~li~~~~~~~~~~~~~~a~~~~~~m~~~g--~~~~--~~~~~~li~~~~--~~g~~~~a~---------~~~~~m~~~~~  118 (385)
                      .+|.-+-.+...+++++|.++++++.+..  ...|  ...|-.|+..-.  -.+..+.+.         ..++.+.... 
T Consensus        14 ~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l~~i~~~~-   92 (378)
T 3q15_A           14 VKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQ-   92 (378)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHHHHHHGGG-
T ss_pred             HHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHHHHHhccC-
Confidence            33443333344899999999999987752  2222  333444443211  112222222         4444432211 


Q ss_pred             cccccchHHHHHHhcCCCCC-C-cc---hHHHHHHHHHhCCCchHHHHHHHHHHHCCC-CC----CHhhHHHHHHHhcCc
Q 040338          119 FCWKFGIIRLLIMFQKMPER-D-LV---SWNTMISILTRHGFGFETLCTFIELWNHGF-GL----SSMLYATAFSARASV  188 (385)
Q Consensus       119 ~~~~~~~~~a~~~~~~~~~~-~-~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p----~~~t~~~ll~~~~~~  188 (385)
                                        .+ + ..   .|......+...|++++|+..|++..+... .+    ...++..+...+...
T Consensus        93 ------------------~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~  154 (378)
T 3q15_A           93 ------------------KKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHM  154 (378)
T ss_dssp             ------------------HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHT
T ss_pred             ------------------CCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHc
Confidence                              11 1 11   222344556789999999999999876421 12    245777888899999


Q ss_pred             cCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----CC-
Q 040338          189 YDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----RN-  262 (385)
Q Consensus       189 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~~-  262 (385)
                      |+++.|...+++..+.........                .....+++.+...|...|++++|++.|++..+     ++ 
T Consensus       155 ~~~~~A~~~~~~al~~~~~~~~~~----------------~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~  218 (378)
T 3q15_A          155 KQTHVSMYHILQALDIYQNHPLYS----------------IRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQND  218 (378)
T ss_dssp             TCHHHHHHHHHHHHHHHHTSTTCH----------------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             CCcHHHHHHHHHHHHHHHhCCCch----------------hhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCH
Confidence            999999999998876422111000                01234567788889999999999999987764     22 


Q ss_pred             ---hhhHHHHHHHHHhcCCCCchHHHH-----------------HHHHHHHHhcccCChhhHHHHHHHHHhccc------
Q 040338          263 ---MISWMVLISAFSQAGVLEKPRFFF-----------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY------  316 (385)
Q Consensus       263 ---~~~~~~li~~~~~~g~~~~a~~~~-----------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------  316 (385)
                         ..++..+...|...|++++|+..+                 ++..+...+.+.|++++|...+++..+...      
T Consensus       219 ~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  298 (378)
T 3q15_A          219 RFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKF  298 (378)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSC
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHH
Confidence               357788889999999999999888                 678888999999999999999999887532      


Q ss_pred             -hhhHHHHHHHHHccCC---HHHHHHHHHhCCCCCC-cchHHHHHHHHHhcCChHHHHHHHHHHHhc
Q 040338          317 -TCYFVCMVDLLGLSGL---LGEAKKLIDEMPSKPT-CVIWGALLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       317 -~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                       ...+..+...+...|+   +.+|...+++....|+ ...+..+...|...|++++|...+++..+.
T Consensus       299 ~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~~  365 (378)
T 3q15_A          299 YKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKA  365 (378)
T ss_dssp             HHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence             4456667777788888   9999999998654333 346678899999999999999999998754

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.19  E-value=2.4e-09  Score=92.98  Aligned_cols=217  Identities=9%  Similarity=-0.065  Sum_probs=152.9

Q ss_pred             hhHHHHHhhhC---CCChhhHHHHHHHHHhh----hccCCh-------HHHHHHHHHHHHhccCCCchHHHhHHHHHHhc
Q 040338           35 DDDYRVFCDIG---PRYLFTYNTMINGGVRC----LCVGNI-------KMALHLHGLVKKFYFVSDESIAKSSIDMHVKC  100 (385)
Q Consensus        35 ~~A~~~~~~~~---~~~~~~~~~li~~~~~~----~~~~~~-------~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  100 (385)
                      +.|..+|++..   +.++..|..+...+...    ...|++       ++|..+|++..+.-.+-+...|..++..+.+.
T Consensus        33 ~~a~~~~~~al~~~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~  112 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR  112 (308)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhc
Confidence            56666776554   44666777777665431    125776       89999999999831233566899999999999


Q ss_pred             CChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcc-hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHH
Q 040338          101 GAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLV-SWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYA  179 (385)
Q Consensus       101 g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~  179 (385)
                      |++++|.++|++..+..                   +.+.. +|..+...+.+.|++++|..+|++..+.. +++...|.
T Consensus       113 ~~~~~A~~~~~~al~~~-------------------p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~  172 (308)
T 2ond_A          113 MKYEKVHSIYNRLLAIE-------------------DIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYV  172 (308)
T ss_dssp             TCHHHHHHHHHHHHTSS-------------------SSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHH
T ss_pred             CCHHHHHHHHHHHHhcc-------------------ccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHH
Confidence            99999999999987644                   22343 89999999999999999999999998753 23444444


Q ss_pred             HHHHH-hcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhc
Q 040338          180 TAFSA-RASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELM  258 (385)
Q Consensus       180 ~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  258 (385)
                      ..... +...|+.++|.++|+..++..+                       .+...|..++..+.+.|++++|..+|++.
T Consensus       173 ~~a~~~~~~~~~~~~A~~~~~~al~~~p-----------------------~~~~~~~~~~~~~~~~g~~~~A~~~~~~a  229 (308)
T 2ond_A          173 TAALMEYYCSKDKSVAFKIFELGLKKYG-----------------------DIPEYVLAYIDYLSHLNEDNNTRVLFERV  229 (308)
T ss_dssp             HHHHHHHHTSCCHHHHHHHHHHHHHHHT-----------------------TCHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCC-----------------------CcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            33322 2236999999999999988642                       12345577777888888999999999988


Q ss_pred             ccC---C----hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc
Q 040338          259 SRR---N----MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY  316 (385)
Q Consensus       259 ~~~---~----~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  316 (385)
                      .+.   +    ...|..++                      ......|+.+.|..+++++.+..+
T Consensus       230 l~~~~l~p~~~~~l~~~~~----------------------~~~~~~g~~~~a~~~~~~a~~~~p  272 (308)
T 2ond_A          230 LTSGSLPPEKSGEIWARFL----------------------AFESNIGDLASILKVEKRRFTAFR  272 (308)
T ss_dssp             HHSSSSCGGGCHHHHHHHH----------------------HHHHHHSCHHHHHHHHHHHHHHTT
T ss_pred             HhccCCCHHHHHHHHHHHH----------------------HHHHHcCCHHHHHHHHHHHHHHcc
Confidence            652   1    12333333                      333445666777777777776655

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.18  E-value=4.7e-10  Score=103.54  Aligned_cols=207  Identities=10%  Similarity=-0.100  Sum_probs=164.8

Q ss_pred             hhhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCCh-HHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHH
Q 040338           33 LIDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNI-KMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAES  108 (385)
Q Consensus        33 ~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~-~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~  108 (385)
                      .++++...++...   ..+...|..+-..+..   .|++ ++|++.|++..+.. +.+...|..+..+|.+.|++++|.+
T Consensus        83 ~~~~al~~l~~~~~~~~~~a~~~~~lg~~~~~---~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~  158 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSAQVEAQALMLKGKALNV---TPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHT  158 (474)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHHTS---SSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccCchhHHHHHHHHHHHHh---ccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            5777777777654   2345566666666555   8999 99999999999875 3367899999999999999999999


Q ss_pred             HHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhC---------CCchHHHHHHHHHHHCCCCC-CHhhH
Q 040338          109 AFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRH---------GFGFETLCTFIELWNHGFGL-SSMLY  178 (385)
Q Consensus       109 ~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~---------~~~~~a~~~~~~m~~~g~~p-~~~t~  178 (385)
                      .|++..+.+                    |+...+..+...+...         |++++|+..|++..+.  .| +...+
T Consensus       159 ~~~~al~~~--------------------p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~  216 (474)
T 4abn_A          159 CFSGALTHC--------------------KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQM--DVLDGRSW  216 (474)
T ss_dssp             HHHHHHTTC--------------------CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHHHHHhhC--------------------CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHh--CCCCHHHH
Confidence            999887654                    5568888999999999         9999999999999885  44 57788


Q ss_pred             HHHHHHhcCc--------cCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhH
Q 040338          179 ATAFSARASV--------YDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQK  250 (385)
Q Consensus       179 ~~ll~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~  250 (385)
                      ..+..++...        |++++|++.++...+..+.                    ...+...|..+...|...|++++
T Consensus       217 ~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~--------------------~~~~~~~~~~lg~~~~~~g~~~~  276 (474)
T 4abn_A          217 YILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRK--------------------ASSNPDLHLNRATLHKYEESYGE  276 (474)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGG--------------------GGGCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCC--------------------cccCHHHHHHHHHHHHHcCCHHH
Confidence            8899999888        9999999999999987421                    00244556778888888999999


Q ss_pred             HHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHH
Q 040338          251 ADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFF  285 (385)
Q Consensus       251 A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~  285 (385)
                      |+..|++..+  | +...+..+...+...|++++|++.
T Consensus       277 A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~  314 (474)
T 4abn_A          277 ALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLES  314 (474)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999998865  3 456677777777777777766544

>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=99.17  E-value=3.1e-10  Score=90.09  Aligned_cols=152  Identities=11%  Similarity=-0.060  Sum_probs=132.9

Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHHhc
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSGCS  296 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~~~  296 (385)
                      ...+..+...+...|++++|...++++.+   .+...+..+...+...|++++|...+            .+..+...+.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~   87 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYV   87 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            34567778888889999999999998876   36678888999999999999999988            7888888999


Q ss_pred             ccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVM  372 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~  372 (385)
                      ..|++++|.+.++++.+..+  ...+..+...+...|++++|.+.+++....  .+...+..+...|...|++++|...+
T Consensus        88 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~  167 (186)
T 3as5_A           88 QVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHF  167 (186)
T ss_dssp             HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999999999988776  778888999999999999999999988663  35678899999999999999999999


Q ss_pred             HHHHhccccCC
Q 040338          373 RNLLQLDVKVF  383 (385)
Q Consensus       373 ~~~~~~~~~~~  383 (385)
                      ++..+..|.++
T Consensus       168 ~~~~~~~~~~~  178 (186)
T 3as5_A          168 KKANELDEGAS  178 (186)
T ss_dssp             HHHHHHHHCCC
T ss_pred             HHHHHcCCCch
Confidence            99998877654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.14  E-value=3.8e-09  Score=94.52  Aligned_cols=219  Identities=8%  Similarity=-0.021  Sum_probs=162.9

Q ss_pred             HHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC--CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCC
Q 040338           93 SIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE--RDLVSWNTMISILTRHGFGFETLCTFIELWNHG  170 (385)
Q Consensus        93 li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  170 (385)
                      ....+...|++++|...|++..+..               ...+.  ....++..+...|...|++++|...+++..+..
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~---------------~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~  171 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKEL---------------PFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIY  171 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTG---------------GGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHH---------------hhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence            4455677899999999998765432               22211  124578888899999999999999999876531


Q ss_pred             -----CCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC-CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHH
Q 040338          171 -----FGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS-LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA  243 (385)
Q Consensus       171 -----~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~  243 (385)
                           ..+ ...++..+..++...|++++|.+.++...+.... ++..                  ....++..+...|.
T Consensus       172 ~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~------------------~~~~~~~~lg~~y~  233 (378)
T 3q15_A          172 QNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDR------------------FIAISLLNIANSYD  233 (378)
T ss_dssp             HTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH------------------HHHHHHHHHHHHHH
T ss_pred             HhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHH------------------HHHHHHHHHHHHHH
Confidence                 122 2457778888999999999999999988764211 1111                  12245677888888


Q ss_pred             cCCChhHHHHHHHhccc-----C---ChhhHHHHHHHHHhcCCCCchHHHH-----------------HHHHHHHHhccc
Q 040338          244 EGGSTQKADLAFELMSR-----R---NMISWMVLISAFSQAGVLEKPRFFF-----------------FFVSLLSGCSHS  298 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~-----~---~~~~~~~li~~~~~~g~~~~a~~~~-----------------~~~~l~~~~~~~  298 (385)
                      ..|++++|+..|++..+     .   ...++..+...|.+.|++++|...+                 .+..+...+...
T Consensus       234 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~  313 (378)
T 3q15_A          234 RSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKET  313 (378)
T ss_dssp             HHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSS
T ss_pred             HCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCC
Confidence            99999999999987765     2   2456777888999999999999888                 566677777788


Q ss_pred             CC---hhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          299 GP---VTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       299 ~~---~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      ++   +.+|...++....... ...+..+...|...|++++|.+.|++..
T Consensus       314 ~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  363 (378)
T 3q15_A          314 VDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVL  363 (378)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            88   7888888877433333 6677789999999999999999998764

>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=99.12  E-value=2.3e-09  Score=84.88  Aligned_cols=154  Identities=11%  Similarity=-0.014  Sum_probs=117.5

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  166 (385)
                      ...+..+...+...|++++|.+.|+++.+.+                   +.+..++..+...+...|++++|...++++
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~   68 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-------------------AFDVDVALHLGIAYVKTGAVDRGTELLERS   68 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-------------------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-------------------ccChHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3567778888999999999999998887655                   356778889999999999999999999999


Q ss_pred             HHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCC
Q 040338          167 WNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGG  246 (385)
Q Consensus       167 ~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g  246 (385)
                      .+. .+.+...+..+...+...|++++|.+.++.+.+....                       +...+..+...+...|
T Consensus        69 ~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-----------------------~~~~~~~~a~~~~~~~  124 (186)
T 3as5_A           69 LAD-APDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEANPI-----------------------NFNVRFRLGVALDNLG  124 (186)
T ss_dssp             HHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-----------------------CHHHHHHHHHHHHHTT
T ss_pred             Hhc-CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcH-----------------------hHHHHHHHHHHHHHcC
Confidence            875 2336778888888999999999999999999887431                       2334566777788888


Q ss_pred             ChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchH
Q 040338          247 STQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       247 ~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~  283 (385)
                      ++++|...+++..+  | +...+..+...+...|++++|.
T Consensus       125 ~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A          125 RFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHH
Confidence            99999999988765  2 3344545555554444444443

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.09  E-value=7.6e-08  Score=85.71  Aligned_cols=285  Identities=8%  Similarity=-0.079  Sum_probs=176.2

Q ss_pred             hhhhHHHHHhhhC----CCChh----hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccC-CC----chHHHhHHHHHHh
Q 040338           33 LIDDDYRVFCDIG----PRYLF----TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFV-SD----ESIAKSSIDMHVK   99 (385)
Q Consensus        33 ~~~~A~~~~~~~~----~~~~~----~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~-~~----~~~~~~li~~~~~   99 (385)
                      ++++|...+++..    ..+..    .++.+-..+..   .|++++|...+++..+.... ++    ..++..+...+..
T Consensus        29 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~  105 (373)
T 1hz4_A           29 NPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHC---KGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFA  105 (373)
T ss_dssp             CHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHh---cCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHH
Confidence            6667766666432    22222    23444444444   79999999999998764221 12    2335667788899


Q ss_pred             cCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC---C-CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCC--C
Q 040338          100 CGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE---R-DLVSWNTMISILTRHGFGFETLCTFIELWNHGFG--L  173 (385)
Q Consensus       100 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~--p  173 (385)
                      .|++++|...+++..+               ...+...   | ...++..+...+...|++++|...+++.......  +
T Consensus       106 ~G~~~~A~~~~~~al~---------------~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  170 (373)
T 1hz4_A          106 QGFLQTAWETQEKAFQ---------------LINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQP  170 (373)
T ss_dssp             TTCHHHHHHHHHHHHH---------------HHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCG
T ss_pred             CCCHHHHHHHHHHHHH---------------HHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCc
Confidence            9999999999976532               2222222   2 2345667788899999999999999998764321  1


Q ss_pred             --CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCch-HHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhH
Q 040338          174 --SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDV-FVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQK  250 (385)
Q Consensus       174 --~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~  250 (385)
                        ...++..+...+...|++++|...+++.......++. ..+...                 .....+..+...|++++
T Consensus       171 ~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~g~~~~  233 (373)
T 1hz4_A          171 QQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISN-----------------ANKVRVIYWQMTGDKAA  233 (373)
T ss_dssp             GGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHH-----------------HHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHH-----------------HHHHHHHHHHHCCCHHH
Confidence              2356777888899999999999999998765322211 111000                 01123345678899999


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHH
Q 040338          251 ADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVC  322 (385)
Q Consensus       251 A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~  322 (385)
                      |...++...+++...             .  ......+..+...+...|++++|...++.......        ...+..
T Consensus       234 A~~~~~~a~~~~~~~-------------~--~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~  298 (373)
T 1hz4_A          234 AANWLRHTAKPEFAN-------------N--HFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLL  298 (373)
T ss_dssp             HHHHHHHSCCCCCTT-------------C--GGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCCc-------------c--hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHH
Confidence            999999887643110             0  00000122334444555566666666665544321        235556


Q ss_pred             HHHHHHccCCHHHHHHHHHhCCCC-----------CCcchHHHHHHHHHhcCChHH
Q 040338          323 MVDLLGLSGLLGEAKKLIDEMPSK-----------PTCVIWGALLGACCSHYNTKL  367 (385)
Q Consensus       323 li~~~~~~g~~~~A~~~~~~m~~~-----------p~~~~~~~li~~~~~~g~~~~  367 (385)
                      +..++...|+.++|...+++....           ........++..+......++
T Consensus       299 la~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~~~~g~~~~~ll~~~~~~~~~~~  354 (373)
T 1hz4_A          299 LNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEAMAQQLRQLIQLNTLPE  354 (373)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTTHHHHHHHHHHHHHTTCSCH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHhccccHHHHHHHccHHHHHHHHHHHhCCCCch
Confidence            677788889999888888776541           112234567777777777633

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.09  E-value=1.7e-08  Score=89.88  Aligned_cols=265  Identities=12%  Similarity=-0.006  Sum_probs=182.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCch----HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC--
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDES----IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER--  138 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~----~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~--  138 (385)
                      .|++++|...+++..+.....+..    +++.+...+...|++++|.+.+++....               ......+  
T Consensus        27 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---------------~~~~~~~~~   91 (373)
T 1hz4_A           27 DGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQM---------------ARQHDVWHY   91 (373)
T ss_dssp             TTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------------HHHTTCHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH---------------HHhcCcHHH
Confidence            799999999999988764222222    4666778888899999999999775432               1221111  


Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHC----CCC--C-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchH
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNH----GFG--L-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVF  211 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~--p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  211 (385)
                      ...+++.+...+...|++++|...+++..+.    +..  | ....+..+...+...|++++|...+++...........
T Consensus        92 ~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  171 (373)
T 1hz4_A           92 ALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQ  171 (373)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGG
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcH
Confidence            1234567778899999999999999988653    222  3 23456677788899999999999999988765432110


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc----CCh-hhHHHHHHHHHhcCCCCchHHHH
Q 040338          212 VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR----RNM-ISWMVLISAFSQAGVLEKPRFFF  286 (385)
Q Consensus       212 ~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~-~~~~~li~~~~~~g~~~~a~~~~  286 (385)
                                        ....++..+...+...|++++|...+++...    ++. ..+...                 
T Consensus       172 ------------------~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~-----------------  216 (373)
T 1hz4_A          172 ------------------QQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISN-----------------  216 (373)
T ss_dssp             ------------------GGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHH-----------------
T ss_pred             ------------------HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHH-----------------
Confidence                              1123556777888889999999999987653    111 011100                 


Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----C---Cc-chH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----P---TC-VIW  352 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p---~~-~~~  352 (385)
                      .....+..+...|+.++|...++.......      ...+..+...+...|++++|...+++....    +   +. ..+
T Consensus       217 ~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~  296 (373)
T 1hz4_A          217 ANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNL  296 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHH
Confidence            111223335567777777777777665433      224567788899999999999999887542    1   12 256


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhcc
Q 040338          353 GALLGACCSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       353 ~~li~~~~~~g~~~~a~~~~~~~~~~~  379 (385)
                      ..+..++...|+.++|...+++.....
T Consensus       297 ~~la~~~~~~g~~~~A~~~l~~al~~~  323 (373)
T 1hz4_A          297 LLLNQLYWQAGRKSDAQRVLLDALKLA  323 (373)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHh
Confidence            677888999999999999999887543

>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=99.08  E-value=5.6e-10  Score=107.51  Aligned_cols=151  Identities=13%  Similarity=0.065  Sum_probs=136.9

Q ss_pred             chhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHH
Q 040338          230 SSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSG  294 (385)
Q Consensus       230 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~  294 (385)
                      .+..+++.|...|.+.|++++|+..|++..+  | +..+|+.+..+|.+.|++++|++.|            +|..+..+
T Consensus         7 ~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~   86 (723)
T 4gyw_A            7 THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNT   86 (723)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3567889999999999999999999998876  4 5789999999999999999999999            89999999


Q ss_pred             hcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHH
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      +...|++++|.+.|++..+..+  ...+..+...|.+.|++++|++.|++..+ .| +...|..+..+|...|++++|.+
T Consensus        87 l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~  166 (723)
T 4gyw_A           87 LKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDE  166 (723)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHH
Confidence            9999999999999999999887  88899999999999999999999998876 35 46689999999999999999999


Q ss_pred             HHHHHHhccc
Q 040338          371 VMRNLLQLDV  380 (385)
Q Consensus       371 ~~~~~~~~~~  380 (385)
                      .++++.+..+
T Consensus       167 ~~~kal~l~~  176 (723)
T 4gyw_A          167 RMKKLVSIVA  176 (723)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhCh
Confidence            9999876543

>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=99.07  E-value=4e-09  Score=89.64  Aligned_cols=238  Identities=12%  Similarity=-0.032  Sum_probs=151.0

Q ss_pred             cCChHHHHHHHHHHHHh-------ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC
Q 040338           65 VGNIKMALHLHGLVKKF-------YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE  137 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~-------g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~  137 (385)
                      .|++++|...+++..+.       ..+....++..+...|...|++++|...+++..+..           .+.+..-.+
T Consensus        14 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-----------~~~~~~~~~   82 (283)
T 3edt_B           14 LVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIR-----------EKTLGKDHP   82 (283)
T ss_dssp             CSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-----------HHHTCTTCH
T ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH-----------HHHcCCcch
Confidence            57777777777776653       112346778889999999999999999997764321           000001112


Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHC------CCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCch
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNH------GFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDV  210 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  210 (385)
                      ....++..+...|...|++++|...|++..+.      .-.| ...++..+...+...|++++|...+++..+..     
T Consensus        83 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-----  157 (283)
T 3edt_B           83 AVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIY-----  157 (283)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH-----
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-----
Confidence            34568889999999999999999999998764      1123 46678889999999999999999999988751     


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC------------ChhhHHHHHHHHHhcCC
Q 040338          211 FVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR------------NMISWMVLISAFSQAGV  278 (385)
Q Consensus       211 ~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~------------~~~~~~~li~~~~~~g~  278 (385)
                                .+....+.+....++..+...|...|++++|...+++..+.            ....+..+...+...+.
T Consensus       158 ----------~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (283)
T 3edt_B          158 ----------ATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDK  227 (283)
T ss_dssp             ----------HHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCC
T ss_pred             ----------HHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCc
Confidence                      00000001123446677888888999999999999887641            11233333333333333


Q ss_pred             CCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          279 LEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       279 ~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      ...+.                .+..+...++......+  ...+..+...|...|++++|.+.|++..
T Consensus       228 ~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  279 (283)
T 3edt_B          228 RRDSA----------------PYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCAS  279 (283)
T ss_dssp             CCC----------------------------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hhHHH----------------HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33221                22333333333322222  5667778888888888888888887654

>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=99.07  E-value=3e-09  Score=90.45  Aligned_cols=152  Identities=11%  Similarity=-0.082  Sum_probs=113.2

Q ss_pred             hhHHHHHhhhCCCC----hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhc------c-CCCchHHHhHHHHHHhcCCh
Q 040338           35 DDDYRVFCDIGPRY----LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFY------F-VSDESIAKSSIDMHVKCGAV  103 (385)
Q Consensus        35 ~~A~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g------~-~~~~~~~~~li~~~~~~g~~  103 (385)
                      ++|..+++++..++    ..++..+-..+..   .|++++|...+++..+..      - +....++..+...|...|++
T Consensus        25 ~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  101 (283)
T 3edt_B           25 KQALEDLEKTSGHDHPDVATMLNILALVYRD---QNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKY  101 (283)
T ss_dssp             HHHHHHHHHHHCSSSHHHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH---cccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccH
Confidence            33444444443333    3456666666655   899999999999998752      1 22456788999999999999


Q ss_pred             hHHHHHHHhccCCCccccccchHHHHHHhcCCC----CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC------CCCC
Q 040338          104 DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMP----ERDLVSWNTMISILTRHGFGFETLCTFIELWNH------GFGL  173 (385)
Q Consensus       104 ~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p  173 (385)
                      ++|.+.|++..+.               +.+..    +....++..+...|...|++++|...|++..+.      +-.|
T Consensus       102 ~~A~~~~~~al~~---------------~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  166 (283)
T 3edt_B          102 KEAEPLCKRALEI---------------REKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDP  166 (283)
T ss_dssp             HHHHHHHHHHHHH---------------HHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCH
T ss_pred             HHHHHHHHHHHHH---------------HHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            9999999776432               22111    223567888999999999999999999998775      2234


Q ss_pred             -CHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          174 -SSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       174 -~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                       ...++..+...+...|++++|...+++..+.
T Consensus       167 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          167 NVAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             3567888999999999999999999998874

>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=99.03  E-value=5.4e-09  Score=86.30  Aligned_cols=153  Identities=8%  Similarity=-0.081  Sum_probs=132.8

Q ss_pred             hhhHHHHHHHHHHcCCChhHHHHHHHhccc----CChhhHHHHHHHHHhcCCCCchHHHH------------HHHHHHHH
Q 040338          231 SIQIGKALVTMYAEGGSTQKADLAFELMSR----RNMISWMVLISAFSQAGVLEKPRFFF------------FFVSLLSG  294 (385)
Q Consensus       231 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~li~~~~~~g~~~~a~~~~------------~~~~l~~~  294 (385)
                      +...+......+...|++++|+..|++..+    ++...+..+..++...|++++|+..+            ++..+...
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~   85 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSAA   85 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHHH
Confidence            446677888889999999999999998765    56677777899999999999999998            88899999


Q ss_pred             hcccCChhhHHHHHHHHHhccc--h-------hhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC---cchHHHHHHHHHh
Q 040338          295 CSHSGPVTKGKHYFTAMAKFTY--T-------CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT---CVIWGALLGACCS  361 (385)
Q Consensus       295 ~~~~~~~~~a~~~~~~~~~~~~--~-------~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~---~~~~~~li~~~~~  361 (385)
                      +...|++++|...+++..+..+  .       ..+..+...+...|++++|++.|++..+. |+   ...|..+...|..
T Consensus        86 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~  165 (228)
T 4i17_A           86 YRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLFYN  165 (228)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHH
Confidence            9999999999999999998777  3       55888888999999999999999999874 65   4678888888888


Q ss_pred             cCCh---------------------------HHHHHHHHHHHhccccCC
Q 040338          362 HYNT---------------------------KLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       362 ~g~~---------------------------~~a~~~~~~~~~~~~~~~  383 (385)
                      .|+.                           ++|+..+++..+..|.+.
T Consensus       166 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l~p~~~  214 (228)
T 4i17_A          166 NGADVLRKATPLASSNKEKYASEKAKADAAFKKAVDYLGEAVTLSPNRT  214 (228)
T ss_dssp             HHHHHHHHHGGGTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCH
Confidence            8888                           899999999999888653

>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=99.01  E-value=7.7e-09  Score=99.62  Aligned_cols=164  Identities=10%  Similarity=-0.036  Sum_probs=128.4

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ..+|+.+-..+..   .|++++|++.|++..+.. +-+...|..+..+|.+.|++++|++.|++..+.+           
T Consensus         9 a~al~nLG~~~~~---~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-----------   73 (723)
T 4gyw_A            9 ADSLNNLANIKRE---QGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-----------   73 (723)
T ss_dssp             HHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-----------
Confidence            4567777777666   899999999999988864 2356788888899999999999999988876544           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                              +.+...|+.+..+|.+.|++++|++.|++..+.  .| +...|..+..++.+.|++++|++.|++.++..+.
T Consensus        74 --------P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~  143 (723)
T 4gyw_A           74 --------PTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD  143 (723)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC
T ss_pred             --------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence                    345778888889999999999999999888774  45 5678888888888999999999999988876531


Q ss_pred             CchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          208 LDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       208 ~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                                             +...+..+...+...|++++|.+.+++..+
T Consensus       144 -----------------------~~~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          144 -----------------------FPDAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             -----------------------CHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             -----------------------ChHHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence                                   234456777777778888888888877653

>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=98.98  E-value=1.4e-08  Score=75.56  Aligned_cols=132  Identities=12%  Similarity=0.063  Sum_probs=110.2

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHH
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLI  130 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~  130 (385)
                      .|..+...+..   .|++++|..+++.+.+.+ +.+...+..+...+...|++++|...|+++.+.+             
T Consensus         3 ~~~~l~~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-------------   65 (136)
T 2fo7_A            3 AWYNLGNAYYK---QGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-------------   65 (136)
T ss_dssp             HHHHHHHHHHH---HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------------
T ss_pred             HHHHHHHHHHH---cCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-------------
Confidence            45666677666   799999999999998875 3467788889999999999999999998876544             


Q ss_pred             HhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          131 MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       131 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                            +.+...+..+...+...|++++|..+++++.+.. +.+...+..+...+...|++++|...++.+.+..+
T Consensus        66 ------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~  134 (136)
T 2fo7_A           66 ------PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP  134 (136)
T ss_dssp             ------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHST
T ss_pred             ------CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHccCC
Confidence                  3566788889999999999999999999998753 33577888899999999999999999999887653

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.96  E-value=1.1e-08  Score=88.02  Aligned_cols=210  Identities=13%  Similarity=0.038  Sum_probs=129.5

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHC----CCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNH----GFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      .|+.....|...|++++|...|++..+.    |-.++ ..+|+.+..+|.+.|++++|+..++..++.            
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l------------  106 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQI------------  106 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH------------
Confidence            3555566677777777777777666442    22222 456667777777777777777777766543            


Q ss_pred             HHHHHhcCCCCCCchhhHHHHHHHHHHcC-CChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHh
Q 040338          217 IDMYLKCGCNGIESSIQIGKALVTMYAEG-GSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGC  295 (385)
Q Consensus       217 i~~~~~~g~~~~~~~~~~~~~li~~~~~~-g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~  295 (385)
                         +.+.|+  ......+++.+...|... |++++|+..|++..+-           +-..++.  ....-++..+...+
T Consensus       107 ---~~~~g~--~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~-----------~~~~~~~--~~~~~~~~~lg~~~  168 (292)
T 1qqe_A          107 ---FTHRGQ--FRRGANFKFELGEILENDLHDYAKAIDCYELAGEW-----------YAQDQSV--ALSNKCFIKCADLK  168 (292)
T ss_dssp             ---HHHTTC--HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH-----------HHHTTCH--HHHHHHHHHHHHHH
T ss_pred             ---HHHcCC--HHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH-----------HHhCCCh--HHHHHHHHHHHHHH
Confidence               112221  011234666677777774 7777777777665431           0001100  00000456667777


Q ss_pred             cccCChhhHHHHHHHHHhccc--h-------hhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcc------hHHHHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY--T-------CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCV------IWGALLGAC  359 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~--~-------~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~------~~~~li~~~  359 (385)
                      ...|++++|...|++..+..+  .       ..+..+..++...|++++|...|++...- |+..      .+..++.+|
T Consensus       169 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~  248 (292)
T 1qqe_A          169 ALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAV  248 (292)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH
Confidence            788888888899998887665  1       14677788899999999999999998763 4322      344556666


Q ss_pred             H--hcCChHHHHHHHHHHHhcccc
Q 040338          360 C--SHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       360 ~--~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      .  ..+++++|+..|+++...+|.
T Consensus       249 ~~~~~~~~~~A~~~~~~~~~l~~~  272 (292)
T 1qqe_A          249 NEGDSEQLSEHCKEFDNFMRLDKW  272 (292)
T ss_dssp             HTTCTTTHHHHHHHHTTSSCCCHH
T ss_pred             HcCCHHHHHHHHHHhccCCccHHH
Confidence            5  456788999988887766653

>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=98.96  E-value=3.7e-08  Score=81.19  Aligned_cols=186  Identities=10%  Similarity=-0.094  Sum_probs=134.6

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      |+..|...-..+..   .|++++|...|+...+...+++...+..+..++...|++++|++.|++..+.+          
T Consensus         6 ~~~~~~~~g~~~~~---~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~----------   72 (228)
T 4i17_A            6 DPNQLKNEGNDALN---AKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN----------   72 (228)
T ss_dssp             CHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT----------
T ss_pred             CHHHHHHHHHHHHH---ccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC----------
Confidence            45556556566555   89999999999999988654677888889999999999999999999887655          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CH-------hhHHHHHHHhcCccCccchhhHHH
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SS-------MLYATAFSARASVYDLEWGPHLHS  199 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~-------~t~~~ll~~~~~~~~~~~a~~~~~  199 (385)
                               +.+..+|..+...+...|++++|+..|++..+.  .| +.       ..|..+-..+...|++++|++.++
T Consensus        73 ---------p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~  141 (228)
T 4i17_A           73 ---------YNLANAYIGKSAAYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYK  141 (228)
T ss_dssp             ---------CSHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ---------cchHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHH
Confidence                     356778999999999999999999999999875  34 33       457777788889999999999999


Q ss_pred             HHHHhCCCC--chHHHHHHHHHHHhcCCCC-------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          200 RVVHMEPSL--DVFVGSGLIDMYLKCGCNG-------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       200 ~~~~~~~~~--~~~~~~~li~~~~~~g~~~-------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                      ..++..+ .  +...+..+..+|...|+.-       ...+...|....  ....+.+++|+..|++..+
T Consensus       142 ~al~~~p-~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~  208 (228)
T 4i17_A          142 HATDVTS-KKWKTDALYSLGVLFYNNGADVLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEAVT  208 (228)
T ss_dssp             HHTTSSC-HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcCC-CcccHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHHhh
Confidence            9987632 2  2456666666666555220       001111222211  1223445778888877754

>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=98.90  E-value=2.3e-08  Score=74.40  Aligned_cols=130  Identities=14%  Similarity=0.062  Sum_probs=105.4

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      ..|..+...+...|++++|..+|+++.+.+                   +.+...+..+...+...|++++|..+++++.
T Consensus         2 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~   62 (136)
T 2fo7_A            2 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-------------------PRSAEAWYNLGNAYYKQGDYDEAIEYYQKAL   62 (136)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHcCcHHHHHHHHHHHHHcC-------------------CcchhHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            357788889999999999999998876544                   3566788888999999999999999999998


Q ss_pred             HCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC
Q 040338          168 NHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS  247 (385)
Q Consensus       168 ~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~  247 (385)
                      ..+ +.+...+..+...+...|++++|.+.++.+.+..+.                       +...+..+...+.+.|+
T Consensus        63 ~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-----------------------~~~~~~~la~~~~~~~~  118 (136)
T 2fo7_A           63 ELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR-----------------------SAEAWYNLGNAYYKQGD  118 (136)
T ss_dssp             HHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-----------------------CHHHHHHHHHHHHTTTC
T ss_pred             HHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-----------------------ChHHHHHHHHHHHHHcc
Confidence            763 335677888888999999999999999999887532                       22344667777888889


Q ss_pred             hhHHHHHHHhccc
Q 040338          248 TQKADLAFELMSR  260 (385)
Q Consensus       248 ~~~A~~~~~~m~~  260 (385)
                      +++|...++++.+
T Consensus       119 ~~~A~~~~~~~~~  131 (136)
T 2fo7_A          119 YDEAIEYYQKALE  131 (136)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9999999988764

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.83  E-value=3.6e-08  Score=83.14  Aligned_cols=153  Identities=13%  Similarity=-0.059  Sum_probs=124.9

Q ss_pred             hhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-C---hhhHHHHHHHHHhcCCCCchHHHH---------------HHH
Q 040338          231 SIQIGKALVTMYAEGGSTQKADLAFELMSR--R-N---MISWMVLISAFSQAGVLEKPRFFF---------------FFV  289 (385)
Q Consensus       231 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~---~~~~~~li~~~~~~g~~~~a~~~~---------------~~~  289 (385)
                      +...+-.+...+.+.|++++|+..|+.+.+  | +   ...+..+..+|.+.|++++|+..+               ++.
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~   93 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEY   93 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHH
Confidence            445566777888899999999999999876  3 3   467788889999999999999988               566


Q ss_pred             HHHHHhcc--------cCChhhHHHHHHHHHhccc--hhhH-----------------HHHHHHHHccCCHHHHHHHHHh
Q 040338          290 SLLSGCSH--------SGPVTKGKHYFTAMAKFTY--TCYF-----------------VCMVDLLGLSGLLGEAKKLIDE  342 (385)
Q Consensus       290 ~l~~~~~~--------~~~~~~a~~~~~~~~~~~~--~~~~-----------------~~li~~~~~~g~~~~A~~~~~~  342 (385)
                      .+..++..        .|++++|...|+++.+..+  ....                 ..+...|.+.|++++|+..|++
T Consensus        94 ~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  173 (261)
T 3qky_A           94 ERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEA  173 (261)
T ss_dssp             HHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            67777777        9999999999999998777  3333                 4568889999999999999999


Q ss_pred             CCCC-CC----cchHHHHHHHHHhc----------CChHHHHHHHHHHHhccccCC
Q 040338          343 MPSK-PT----CVIWGALLGACCSH----------YNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       343 m~~~-p~----~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +... |+    ...+..+..+|...          |++++|...++++.+..|..+
T Consensus       174 ~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~  229 (261)
T 3qky_A          174 VFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDSP  229 (261)
T ss_dssp             HHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCCh
Confidence            8763 54    34677788888866          889999999999999887653

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.81  E-value=1.1e-07  Score=78.20  Aligned_cols=181  Identities=9%  Similarity=-0.060  Sum_probs=113.9

Q ss_pred             HHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHh
Q 040338          178 YATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFEL  257 (385)
Q Consensus       178 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  257 (385)
                      +..+...+.+.|++++|+..|+.+++..+...                    .....+..+..+|.+.|++++|+..|++
T Consensus         7 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~--------------------~~~~a~~~lg~~~~~~~~~~~A~~~~~~   66 (225)
T 2yhc_A            7 IYATAQQKLQDGNWRQAITQLEALDNRYPFGP--------------------YSQQVQLDLIYAYYKNADLPLAQAAIDR   66 (225)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTST--------------------THHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCh--------------------HHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            33444556666777777777777766543211                    0112334556666677777777777777


Q ss_pred             ccc--CCh----hhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhH---------
Q 040338          258 MSR--RNM----ISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYF---------  320 (385)
Q Consensus       258 m~~--~~~----~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~---------  320 (385)
                      ..+  |+.    ..+..+..++...|..  +..  .|..+...+...|+.++|...|+++.+..+  ....         
T Consensus        67 ~l~~~P~~~~~~~a~~~~g~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~  142 (225)
T 2yhc_A           67 FIRLNPTHPNIDYVMYMRGLTNMALDDS--ALQ--GFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFL  142 (225)
T ss_dssp             HHHHCTTCTTHHHHHHHHHHHHHHHHC------------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHH
T ss_pred             HHHHCcCCCcHHHHHHHHHHHHHhhhhh--hhh--hhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHH
Confidence            764  322    1344444444443321  100  223334445567788888888888888766  2222         


Q ss_pred             --------HHHHHHHHccCCHHHHHHHHHhCCCC-CCc----chHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          321 --------VCMVDLLGLSGLLGEAKKLIDEMPSK-PTC----VIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       321 --------~~li~~~~~~g~~~~A~~~~~~m~~~-p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                              ..+...|.+.|++++|+..|+++.+. |+.    ..+..+..+|.+.|+.++|.+.++.+...+|..
T Consensus       143 ~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~  217 (225)
T 2yhc_A          143 KDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT  217 (225)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCC
T ss_pred             HHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCc
Confidence                    24566788999999999999998764 553    468889999999999999999999999887764

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.80  E-value=5.3e-07  Score=76.74  Aligned_cols=199  Identities=10%  Similarity=0.022  Sum_probs=134.7

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      |....+..+...+ ..+    |+..|++....+ .++..++..+..++...|++++|++++...+..+..+         
T Consensus        69 ~~~~a~~~la~~~-~~~----a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~---------  133 (310)
T 3mv2_B           69 KLGKVLDLYVQFL-DTK----NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAE---------  133 (310)
T ss_dssp             TTHHHHHHHHHHH-TTT----CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCST---------
T ss_pred             HHHHHHHHHHHHh-ccc----HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCc---------
Confidence            4444444444433 322    678888777654 4566666678888899999999999999886665321         


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCC-------hhhHHHHHHHHHhcCCCCchHHHHHHHH
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRN-------MISWMVLISAFSQAGVLEKPRFFFFFVS  290 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~-------~~~~~~li~~~~~~g~~~~a~~~~~~~~  290 (385)
                                  -+...+..++..+.+.|+.+.|.+.+++|.+.+       ..+...|+.+++..              
T Consensus       134 ------------~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l--------------  187 (310)
T 3mv2_B          134 ------------GTTELLLLAIEVALLNNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKF--------------  187 (310)
T ss_dssp             ------------THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH--------------
T ss_pred             ------------CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHH--------------
Confidence                        133445677788888889999999999997622       34444555553221              


Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-----------C-CcchHHHHHH
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-----------P-TCVIWGALLG  357 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----------p-~~~~~~~li~  357 (385)
                          ....++...|..+|+++....+ ......++.++.+.|++++|.+.++.+.+.           | |..+...+|.
T Consensus       188 ----~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~  263 (310)
T 3mv2_B          188 ----ATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQIT  263 (310)
T ss_dssp             ----HHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHH
T ss_pred             ----HhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHH
Confidence                1112356777888999877765 234445555889999999999999876541           3 4556656666


Q ss_pred             HHHhcCChHHHHHHHHHHHhccccCC
Q 040338          358 ACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       358 ~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .....|+  +|.++++++++..|..+
T Consensus       264 l~~~lgk--~a~~l~~qL~~~~P~hp  287 (310)
T 3mv2_B          264 LALMQGL--DTEDLTNQLVKLDHEHA  287 (310)
T ss_dssp             HHHHTTC--TTHHHHHHHHHTTCCCH
T ss_pred             HHHHhCh--HHHHHHHHHHHhCCCCh
Confidence            6666676  88999999998887654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.80  E-value=5.5e-08  Score=83.59  Aligned_cols=143  Identities=13%  Similarity=0.041  Sum_probs=109.5

Q ss_pred             HHHHcCCChhHHHHHHHhccc-----CC----hhhHHHHHHHHHhcCCCCchHHHH------------------HHHHHH
Q 040338          240 TMYAEGGSTQKADLAFELMSR-----RN----MISWMVLISAFSQAGVLEKPRFFF------------------FFVSLL  292 (385)
Q Consensus       240 ~~~~~~g~~~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~  292 (385)
                      ..|...|++++|...|++..+     .+    ..+|+.+..+|.+.|++++|+..+                  ++..+.
T Consensus        45 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg  124 (292)
T 1qqe_A           45 TIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELG  124 (292)
T ss_dssp             HHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            345566788888877776543     11    357777888888888888887777                  677888


Q ss_pred             HHhccc-CChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC---cc-----hHHH
Q 040338          293 SGCSHS-GPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT---CV-----IWGA  354 (385)
Q Consensus       293 ~~~~~~-~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~---~~-----~~~~  354 (385)
                      ..|... |++++|...|++..+..+        ..++..+...|.+.|++++|+..|++..+. |+   ..     .|..
T Consensus       125 ~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  204 (292)
T 1qqe_A          125 EILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLK  204 (292)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHH
T ss_pred             HHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Confidence            888886 999999999999887544        356788899999999999999999987653 22   11     5677


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          355 LLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       355 li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +..++...|++++|...+++..+..|..
T Consensus       205 lg~~~~~~g~~~~A~~~~~~al~l~p~~  232 (292)
T 1qqe_A          205 KGLCQLAATDAVAAARTLQEGQSEDPNF  232 (292)
T ss_dssp             HHHHHHHTTCHHHHHHHHHGGGCC----
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhCCCC
Confidence            8888999999999999999998877753

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.78  E-value=1.5e-06  Score=80.17  Aligned_cols=341  Identities=10%  Similarity=0.017  Sum_probs=205.6

Q ss_pred             cCC-ChHHHHHHHHHHHHcccchhhHHhhhhhHHHHHhhhC--CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh-
Q 040338            6 SLK-SLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIG--PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF-   81 (385)
Q Consensus         6 ~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~-   81 (385)
                      +.| +++.||.++++++..-+.     .+++.+..+|++-.  .|++..|...+.-..+..  ...+....+|+..+.. 
T Consensus         6 ~~~~~i~~aR~vyer~l~~~P~-----~~~e~~~~iferal~~~ps~~LW~~Y~~f~~~~~--~~~~~i~~~fe~al~~v   78 (493)
T 2uy1_A            6 KMGVELSSPSAIMEHARRLYMS-----KDYRSLESLFGRCLKKSYNLDLWMLYIEYVRKVS--QKKFKLYEVYEFTLGQF   78 (493)
T ss_dssp             ------CCHHHHHHHHHHHHHT-----TCHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHC------CTHHHHHHHHHHS
T ss_pred             HcCcchHHHHHHHHHHHHHCCC-----CCHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhC--chHHHHHHHHHHHHHHc
Confidence            346 488999999999875422     57899999998766  578888888887655531  1345667788877765 


Q ss_pred             ccCC-CchHHHhHHHHHH----hcCChhHHHHHHHhccCCCccc----cc----------------------cchHHHHH
Q 040338           82 YFVS-DESIAKSSIDMHV----KCGAVDYAESAFLRMLNPSLFC----WK----------------------FGIIRLLI  130 (385)
Q Consensus        82 g~~~-~~~~~~~li~~~~----~~g~~~~a~~~~~~m~~~~~~~----~~----------------------~~~~~a~~  130 (385)
                      |..| +...|...+..+.    ..++++.+.++|++........    |.                      ..+..|..
T Consensus        79 g~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~  158 (493)
T 2uy1_A           79 ENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQ  158 (493)
T ss_dssp             TTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHH
Confidence            5333 5567777776553    3467888889998886532211    11                      00111121


Q ss_pred             HhcCCC----CCCcchHHHHHHHHHhCCC-------chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHH
Q 040338          131 MFQKMP----ERDLVSWNTMISILTRHGF-------GFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHS  199 (385)
Q Consensus       131 ~~~~~~----~~~~~~~~~li~~~~~~~~-------~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  199 (385)
                      ++....    ..+...|...+..-...+.       .+.+..+|+++... .+-+...|...+..+.+.|+.+.|..+++
T Consensus       159 ~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~e  237 (493)
T 2uy1_A          159 RYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVE  237 (493)
T ss_dssp             HHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            111111    1133355554444322211       23466788888775 33356666666667778899999999999


Q ss_pred             HHHHhCCCCchHHHHHHHHH----------HHhc--CC------CCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC
Q 040338          200 RVVHMEPSLDVFVGSGLIDM----------YLKC--GC------NGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR  261 (385)
Q Consensus       200 ~~~~~~~~~~~~~~~~li~~----------~~~~--g~------~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  261 (385)
                      +....  +.+...+......          +.+.  +.      .........|...+....+.++++.|..+|+....|
T Consensus       238 rAi~~--P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~~  315 (493)
T 2uy1_A          238 RGIEM--SDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIELGNE  315 (493)
T ss_dssp             HHHHH--CCSSHHHHHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTS
T ss_pred             HHHhC--CCcHHHHHHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhCC
Confidence            99988  3333333221111          0000  00      001112245566666666667788888888777323


Q ss_pred             ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHH
Q 040338          262 NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKL  339 (385)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~  339 (385)
                      + .++.                 +|...+.++... .++.+.|..+|+...+..+  +..+...++...+.|+.+.|..+
T Consensus       316 ~-~~~~-----------------v~i~~A~lE~~~-~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~~~aR~l  376 (493)
T 2uy1_A          316 G-VGPH-----------------VFIYCAFIEYYA-TGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENARAL  376 (493)
T ss_dssp             C-CCHH-----------------HHHHHHHHHHHH-HCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             C-CChH-----------------HHHHHHHHHHHH-CCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            2 1221                 111112222222 2368899999999887665  55566778888889999999999


Q ss_pred             HHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          340 IDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       340 ~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      |+....  ....|...+..-.+.|+.+.+..++++..+
T Consensus       377 ~er~~k--~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          377 FKRLEK--TSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHSCC--BHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHH--HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999853  567788888888889999999998888764

>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=98.76  E-value=8.7e-06  Score=77.67  Aligned_cols=68  Identities=15%  Similarity=0.164  Sum_probs=56.7

Q ss_pred             CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC---hhHHHHHHHhccCCC
Q 040338           46 PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA---VDYAESAFLRMLNPS  117 (385)
Q Consensus        46 ~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~~  117 (385)
                      +.|..+|..+|.....   .+.++.+..+|+.+... ++.....|...+..-.+.|+   .+.+..+|++.....
T Consensus        63 p~d~~~W~~yi~~~~~---~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~  133 (679)
T 4e6h_A           63 PTDIFLYVKLLKHHVS---LKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKE  133 (679)
T ss_dssp             TTCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSS
T ss_pred             cCCHHHHHHHHHHHHh---cCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhc
Confidence            4578899999998665   79999999999999987 56678889999998888888   999999999987644

>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=98.76  E-value=1.2e-07  Score=91.54  Aligned_cols=172  Identities=8%  Similarity=-0.072  Sum_probs=137.4

Q ss_pred             cCChHHHHHHHHHHH--------HhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCC
Q 040338           65 VGNIKMALHLHGLVK--------KFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMP  136 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~--------~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~  136 (385)
                      .|++++|++.+++..        +. .+.+...+..+..+|.+.|++++|++.|++..+.+                   
T Consensus       404 ~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-------------------  463 (681)
T 2pzi_A          404 LSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-------------------  463 (681)
T ss_dssp             TCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-------------------
T ss_pred             ccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-------------------
Confidence            799999999999998        43 24467889999999999999999999999887655                   


Q ss_pred             CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          137 ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       137 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                      +.+...|..+..++...|++++|+..|++..+.  .| +...+..+..++.+.|++++ ++.|++.++..+.        
T Consensus       464 p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~--------  532 (681)
T 2pzi_A          464 GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG--------  532 (681)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT--------
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc--------
Confidence            457788999999999999999999999999885  45 56778889999999999999 9999999987542        


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCch
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKP  282 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a  282 (385)
                                     +...|..+..++.+.|++++|+..|++..+  | +...+..+..++...++.+++
T Consensus       533 ---------------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~  587 (681)
T 2pzi_A          533 ---------------VISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEV  587 (681)
T ss_dssp             ---------------CHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC-------C
T ss_pred             ---------------hHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCCCCCC
Confidence                           334567788888899999999999999976  3 345676777777666654444

>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=98.74  E-value=1.3e-07  Score=81.79  Aligned_cols=231  Identities=10%  Similarity=-0.062  Sum_probs=142.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|.+++++..+... ..      +   +...+++++|...|.+                                
T Consensus         4 ~~~~~eA~~~~~~a~k~~~-~~------~---~~~~~~~~~A~~~~~~--------------------------------   41 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLK-TS------F---MKWKPDYDSAASEYAK--------------------------------   41 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-CC------S---SSCSCCHHHHHHHHHH--------------------------------
T ss_pred             cchHHHHHHHHHHHHHHcc-cc------c---cCCCCCHHHHHHHHHH--------------------------------
Confidence            5778888888887776422 11      0   1114667777666543                                


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHC----CCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNH----GFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDM  219 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  219 (385)
                       ....|...|++++|...|.+..+.    |-.+ -..+|..+...|.+.|++++|+..+++.++.-..            
T Consensus        42 -a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~------------  108 (307)
T 2ifu_A           42 -AAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVE------------  108 (307)
T ss_dssp             -HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHT------------
T ss_pred             -HHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH------------
Confidence             456777889999999998887653    2111 1457788888899999999999999987764211            


Q ss_pred             HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccC
Q 040338          220 YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSG  299 (385)
Q Consensus       220 ~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~  299 (385)
                         .|+  ......++..+...|.. |++++|+..|++..+-           +-..|+..  ....++..+...+...|
T Consensus       109 ---~g~--~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~-----------~~~~~~~~--~~~~~~~~lg~~~~~~g  169 (307)
T 2ifu_A          109 ---NGT--PDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAV-----------FENEERLR--QAAELIGKASRLLVRQQ  169 (307)
T ss_dssp             ---TTC--HHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHH-----------HHHTTCHH--HHHHHHHHHHHHHHHTT
T ss_pred             ---cCC--HHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHH-----------HHhCCChh--HHHHHHHHHHHHHHHcC
Confidence               110  00123456777788878 9999999999877541           11111100  00114455555666666


Q ss_pred             ChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcc------hHHHHHHHHHhcCCh
Q 040338          300 PVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCV------IWGALLGACCSHYNT  365 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~------~~~~li~~~~~~g~~  365 (385)
                      ++++|+..|++......        ...+..++.++...|++++|...|++....|+..      ....++.++ ..|+.
T Consensus       170 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~p~~~~~~e~~~l~~l~~~~-~~~d~  248 (307)
T 2ifu_A          170 KFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESYSIPGFSGSEDCAALEDLLQAY-DEQDE  248 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTSTTSHHHHHHHHHHHHH-HTTCH
T ss_pred             CHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH-HhcCH
Confidence            66666776766665432        2355666777777889999998888876224321      244455555 45666


Q ss_pred             HHHHH
Q 040338          366 KLAEL  370 (385)
Q Consensus       366 ~~a~~  370 (385)
                      +.+..
T Consensus       249 ~~~~~  253 (307)
T 2ifu_A          249 EQLLR  253 (307)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55544

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.72  E-value=1.7e-07  Score=79.05  Aligned_cols=195  Identities=7%  Similarity=-0.072  Sum_probs=115.2

Q ss_pred             CCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC---cchHHHHHHHHHhCCCchHHHH
Q 040338           85 SDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD---LVSWNTMISILTRHGFGFETLC  161 (385)
Q Consensus        85 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~a~~  161 (385)
                      .+...+-.+...+.+.|++++|...|+++.+..+                   .+   ...+..+..+|.+.|++++|+.
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p-------------------~~~~~~~a~~~lg~~~~~~~~~~~A~~   73 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGR-------------------THEWAADAQFYLARAYYQNKEYLLAAS   73 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCS-------------------CSTTHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCC-------------------CCcchHHHHHHHHHHHHHhCcHHHHHH
Confidence            3456667777788888999999998888766542                   22   5567778888888899999999


Q ss_pred             HHHHHHHCCC-CCC-HhhHHHHHHHhcC--------ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCch
Q 040338          162 TFIELWNHGF-GLS-SMLYATAFSARAS--------VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESS  231 (385)
Q Consensus       162 ~~~~m~~~g~-~p~-~~t~~~ll~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~  231 (385)
                      .|++..+... .|. ...+..+..++..        .|++++|+..|+.+++..+.. ......+.......+     ..
T Consensus        74 ~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~-~~~~~a~~~~~~~~~-----~~  147 (261)
T 3qky_A           74 EYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNH-ELVDDATQKIRELRA-----KL  147 (261)
T ss_dssp             HHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTC-TTHHHHHHHHHHHHH-----HH
T ss_pred             HHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCc-hhHHHHHHHHHHHHH-----HH
Confidence            9988887521 122 3445566666766        888888888888888775421 111111100000000     00


Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhccc--CC----hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSR--RN----MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGK  305 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~----~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~  305 (385)
                      ...+..+...|.+.|++++|+..|+...+  |+    ...+..+..+|...|+.+.+.            ...|++++|.
T Consensus       148 ~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~------------~~~~~~~~A~  215 (261)
T 3qky_A          148 ARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRA------------RQPERYRRAV  215 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGG------------GHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhh------------cccchHHHHH
Confidence            11234455666677777777777776654  32    123444445555444333221            1235556666


Q ss_pred             HHHHHHHhccc
Q 040338          306 HYFTAMAKFTY  316 (385)
Q Consensus       306 ~~~~~~~~~~~  316 (385)
                      ..++++.+..+
T Consensus       216 ~~~~~~~~~~p  226 (261)
T 3qky_A          216 ELYERLLQIFP  226 (261)
T ss_dssp             HHHHHHHHHCT
T ss_pred             HHHHHHHHHCC
Confidence            66666655544

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.71  E-value=7.3e-07  Score=76.30  Aligned_cols=176  Identities=10%  Similarity=-0.057  Sum_probs=124.3

Q ss_pred             hHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccC
Q 040338           36 DDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLN  115 (385)
Q Consensus        36 ~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  115 (385)
                      .....++...+.+...+..+-..+..   .|++++|...+++..+.. +-+...+..+...+.+.|++++|...+++...
T Consensus       104 ~l~~~l~~~lp~~~~~~~~~a~~~~~---~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~  179 (287)
T 3qou_A          104 AIRALLDXVLPREEELXAQQAMQLMQ---ESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPL  179 (287)
T ss_dssp             HHHHHHHHHSCCHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCG
T ss_pred             HHHHHHHHHcCCchhhHHHHHHHHHh---CCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCch
Confidence            34444444443334444444445444   899999999999998874 33677888899999999999999999988765


Q ss_pred             CCccccccchHHHHHHhcCCCCCCcchHH-HHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccc
Q 040338          116 PSLFCWKFGIIRLLIMFQKMPERDLVSWN-TMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEW  193 (385)
Q Consensus       116 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~  193 (385)
                      .+                    |+..... .....+.+.++.++|...|++....  .| +...+..+...+...|++++
T Consensus       180 ~~--------------------p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~--~P~~~~~~~~la~~l~~~g~~~~  237 (287)
T 3qou_A          180 QD--------------------QDTRYQGLVAQIELLXQAADTPEIQQLQQQVAE--NPEDAALATQLALQLHQVGRNEE  237 (287)
T ss_dssp             GG--------------------CSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             hh--------------------cchHHHHHHHHHHHHhhcccCccHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHH
Confidence            43                    4333222 2233466778888899999888775  44 57788888899999999999


Q ss_pred             hhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhc
Q 040338          194 GPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELM  258 (385)
Q Consensus       194 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  258 (385)
                      |...+..+++..+..                     .+...+..++..+...|+.++|...|++-
T Consensus       238 A~~~l~~~l~~~p~~---------------------~~~~a~~~l~~~~~~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          238 ALELLFGHLRXDLTA---------------------ADGQTRXTFQEILAALGTGDALASXYRRQ  281 (287)
T ss_dssp             HHHHHHHHHHHCTTG---------------------GGGHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhccccc---------------------ccchHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            999999999886532                     12334566666677777888887777643

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.71  E-value=6.5e-07  Score=76.22  Aligned_cols=146  Identities=8%  Similarity=-0.122  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHH
Q 040338           71 ALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISIL  150 (385)
Q Consensus        71 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  150 (385)
                      ++..+++..+.+ +++..++..+..++...|++++|++++.+....+..                 .-+...+-.++..+
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~-----------------~~~lea~~l~vqi~  146 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEA-----------------EGTTELLLLAIEVA  146 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCS-----------------TTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCC-----------------cCcHHHHHHHHHHH
Confidence            566677666654 445556667778888899999999999887554410                 13566778888999


Q ss_pred             HhCCCchHHHHHHHHHHHCCCCC-----CHhhHHHHHHH--hcC--ccCccchhhHHHHHHHhCCCCchHHHHHHHHHHH
Q 040338          151 TRHGFGFETLCTFIELWNHGFGL-----SSMLYATAFSA--RAS--VYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYL  221 (385)
Q Consensus       151 ~~~~~~~~a~~~~~~m~~~g~~p-----~~~t~~~ll~~--~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  221 (385)
                      .+.|+++.|.+.+++|.+.  .|     +..+...+..+  ...  .++..+|..+|+++.+..  |+...         
T Consensus       147 L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~--p~~~~---------  213 (310)
T 3mv2_B          147 LLNNNVSTASTIFDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--PTWKT---------  213 (310)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--CSHHH---------
T ss_pred             HHCCCHHHHHHHHHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--CCccc---------
Confidence            9999999999999999774  56     35565666655  222  348899999999986653  22111         


Q ss_pred             hcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          222 KCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       222 ~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                                   -..++.++.+.|++++|...++.+.+
T Consensus       214 -------------~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          214 -------------QLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             -------------HHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             -------------HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                         12233366777899999999986543

>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=98.70  E-value=2.9e-07  Score=75.00  Aligned_cols=150  Identities=10%  Similarity=-0.120  Sum_probs=125.7

Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhcccC-ChhhHHHHHHHHHhcC----CCCchHHHH----------HHHHHHHHhc
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSRR-NMISWMVLISAFSQAG----VLEKPRFFF----------FFVSLLSGCS  296 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~g----~~~~a~~~~----------~~~~l~~~~~  296 (385)
                      ...+..+...|...+++++|+..|++..+. +...+..|...|.. +    ++++|+..|          ++..+...|.
T Consensus        18 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g~~~a~~~Lg~~y~   96 (212)
T 3rjv_A           18 RRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAGSKSGEIVLARVLV   96 (212)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            344566777777788999999999988764 67788888888887 6    788899888          7777888887


Q ss_pred             c----cCChhhHHHHHHHHHhccc----hhhHHHHHHHHHc----cCCHHHHHHHHHhCCCC-CCcchHHHHHHHHHhc-
Q 040338          297 H----SGPVTKGKHYFTAMAKFTY----TCYFVCMVDLLGL----SGLLGEAKKLIDEMPSK-PTCVIWGALLGACCSH-  362 (385)
Q Consensus       297 ~----~~~~~~a~~~~~~~~~~~~----~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~-p~~~~~~~li~~~~~~-  362 (385)
                      .    .+++++|...|++..+.+.    +..+..|...|..    .+++++|.+.|++..+. ++...+..|...|... 
T Consensus        97 ~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~a~~~Lg~~y~~g~  176 (212)
T 3rjv_A           97 NRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLSRTGYAEYWAGMMFQQGE  176 (212)
T ss_dssp             CGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTSCTTHHHHHHHHHHHHCB
T ss_pred             cCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCC
Confidence            7    8999999999999999998    7888889999988    88999999999998765 5677888888888764 


Q ss_pred             C-----ChHHHHHHHHHHHhccccC
Q 040338          363 Y-----NTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       363 g-----~~~~a~~~~~~~~~~~~~~  382 (385)
                      |     +.++|..++++..+.|...
T Consensus       177 gg~~~~d~~~A~~~~~~A~~~g~~~  201 (212)
T 3rjv_A          177 KGFIEPNKQKALHWLNVSCLEGFDT  201 (212)
T ss_dssp             TTTBCCCHHHHHHHHHHHHHHTCHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCHH
Confidence            3     8999999999998887643

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.67  E-value=1.3e-07  Score=76.91  Aligned_cols=147  Identities=9%  Similarity=-0.026  Sum_probs=114.4

Q ss_pred             HHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHH----------------HHHHHHhcCCCCchHHHH----------
Q 040338          236 KALVTMYAEGGSTQKADLAFELMSR--R-NMISWMV----------------LISAFSQAGVLEKPRFFF----------  286 (385)
Q Consensus       236 ~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~----------------li~~~~~~g~~~~a~~~~----------  286 (385)
                      -.....+...|++++|+..|+...+  | +...|..                +..+|.+.|++++|+..+          
T Consensus         8 ~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~   87 (208)
T 3urz_A            8 LQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAPNN   87 (208)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Confidence            3445667788999999999998876  3 3455666                888999999999999998          


Q ss_pred             --HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCC--HHHHHHHHHhCCCC-CCcchHHHHHHHH
Q 040338          287 --FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGL--LGEAKKLIDEMPSK-PTCVIWGALLGAC  359 (385)
Q Consensus       287 --~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~--~~~A~~~~~~m~~~-p~~~~~~~li~~~  359 (385)
                        .+..+...+...|++++|...|++..+..+  ...+..+...|...|+  ...+...++..... |....+.....++
T Consensus        88 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~  167 (208)
T 3urz_A           88 VDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARYRDGLSK  167 (208)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHHHHHHHH
Confidence              888999999999999999999999999888  7788888888766554  45566777666543 2223344456677


Q ss_pred             HhcCChHHHHHHHHHHHhccccC
Q 040338          360 CSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       360 ~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ...|++++|...|++.++..|.+
T Consensus       168 ~~~~~~~~A~~~~~~al~l~P~~  190 (208)
T 3urz_A          168 LFTTRYEKARNSLQKVILRFPST  190 (208)
T ss_dssp             HHHHTHHHHHHHHHHHTTTSCCH
T ss_pred             HHccCHHHHHHHHHHHHHhCCCH
Confidence            77899999999999999988864

>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=98.65  E-value=4e-07  Score=87.83  Aligned_cols=171  Identities=12%  Similarity=-0.003  Sum_probs=130.5

Q ss_pred             HhCCCchHHHHHHHHHHH------CCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          151 TRHGFGFETLCTFIELWN------HGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       151 ~~~~~~~~a~~~~~~m~~------~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      ...|++++|++.+++..+      ....| +...+..+..++...|++++|++.++...+...                 
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-----------------  464 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVG-----------------  464 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-----------------
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCc-----------------
Confidence            778999999999999871      01334 566788888899999999999999999988743                 


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH------------HH
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF------------FF  288 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~------------~~  288 (385)
                            .+...|..+...+...|++++|+..|++..+  | +...|..+..+|.+.|++++ ++.+            .|
T Consensus       465 ------~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~  537 (681)
T 2pzi_A          465 ------WRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAA  537 (681)
T ss_dssp             ------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHH
T ss_pred             ------chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHH
Confidence                  2344567777888888999999999998875  4 56788889999999999988 8777            67


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC--------CHHHHHHHHHhCCC
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG--------LLGEAKKLIDEMPS  345 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g--------~~~~A~~~~~~m~~  345 (385)
                      ..+..++...|++++|.+.|++..+..+  ...+..+..++...+        ++++|.+.++.+..
T Consensus       538 ~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~~  604 (681)
T 2pzi_A          538 FGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALPP  604 (681)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSCT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCCC
Confidence            7777888888888888888888777666  556666666665533        36666666666653

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.64  E-value=4e-07  Score=77.98  Aligned_cols=160  Identities=8%  Similarity=-0.082  Sum_probs=126.5

Q ss_pred             cCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHH
Q 040338           83 FVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCT  162 (385)
Q Consensus        83 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  162 (385)
                      .+.+...+..+...+.+.|++++|...|++..+.+                   +.+...+..+...+.+.|++++|...
T Consensus       113 lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-------------------P~~~~a~~~la~~~~~~g~~~~A~~~  173 (287)
T 3qou_A          113 LPREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-------------------NQNGEIGLLLAETLIALNRSEDAEAV  173 (287)
T ss_dssp             SCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-------------------TSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-------------------CcchhHHHHHHHHHHHCCCHHHHHHH
Confidence            35566778888889999999999999999887655                   35677899999999999999999999


Q ss_pred             HHHHHHCCCCCCHhhHHH-HHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHH
Q 040338          163 FIELWNHGFGLSSMLYAT-AFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTM  241 (385)
Q Consensus       163 ~~~m~~~g~~p~~~t~~~-ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~  241 (385)
                      +++....  .|+...... ....+...++.+.|...+++.....+                       .+...+..+...
T Consensus       174 l~~~~~~--~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P-----------------------~~~~~~~~la~~  228 (287)
T 3qou_A          174 LXTIPLQ--DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENP-----------------------EDAALATQLALQ  228 (287)
T ss_dssp             HTTSCGG--GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCT-----------------------TCHHHHHHHHHH
T ss_pred             HHhCchh--hcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCC-----------------------ccHHHHHHHHHH
Confidence            9988664  455443322 23346677888889999999888754                       234456778888


Q ss_pred             HHcCCChhHHHHHHHhccc--CC---hhhHHHHHHHHHhcCCCCchHHHH
Q 040338          242 YAEGGSTQKADLAFELMSR--RN---MISWMVLISAFSQAGVLEKPRFFF  286 (385)
Q Consensus       242 ~~~~g~~~~A~~~~~~m~~--~~---~~~~~~li~~~~~~g~~~~a~~~~  286 (385)
                      +...|++++|+..|....+  |+   ...+..+...|...|+.++|...+
T Consensus       229 l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~  278 (287)
T 3qou_A          229 LHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXY  278 (287)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHH
Confidence            8889999999999999876  42   567888999999999988887665

>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=98.64  E-value=4.2e-07  Score=78.67  Aligned_cols=142  Identities=10%  Similarity=-0.049  Sum_probs=112.8

Q ss_pred             HHHHHcCCChhHHHHHHHhccc-----CC----hhhHHHHHHHHHhcCCCCchHHHH------------------HHHHH
Q 040338          239 VTMYAEGGSTQKADLAFELMSR-----RN----MISWMVLISAFSQAGVLEKPRFFF------------------FFVSL  291 (385)
Q Consensus       239 i~~~~~~g~~~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l  291 (385)
                      ...|...|++++|...|.+..+     .+    ..+|+.+...|...|++++|+..+                  ++..+
T Consensus        43 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~l  122 (307)
T 2ifu_A           43 AVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRA  122 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3456677888888888877654     11    357788888899999999998887                  67788


Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CC----cchHHHH
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PT----CVIWGAL  355 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~----~~~~~~l  355 (385)
                      ...|.. |++++|...+++......        ..++..+...|.+.|++++|+..|++....    ++    ...+..+
T Consensus       123 g~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  201 (307)
T 2ifu_A          123 GKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQ  201 (307)
T ss_dssp             HHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHH
Confidence            888888 999999999998876543        467788899999999999999999988652    22    2356677


Q ss_pred             HHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          356 LGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       356 i~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..++...|++++|...+++.. ..|..
T Consensus       202 g~~~~~~g~~~~A~~~~~~al-~~p~~  227 (307)
T 2ifu_A          202 VLVQLHRADYVAAQKCVRESY-SIPGF  227 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHT-TSTTS
T ss_pred             HHHHHHcCCHHHHHHHHHHHh-CCCCC
Confidence            778888899999999999998 66643

>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=98.63  E-value=3.7e-07  Score=71.89  Aligned_cols=154  Identities=6%  Similarity=-0.124  Sum_probs=91.8

Q ss_pred             HHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338           89 IAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus        89 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      .+..+...+.+.|++++|...|++..+.+                   +.+...+..+...+.+.|++++|+..|++...
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-------------------P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~   68 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL-------------------QSRGDVKLAKADCLLETKQFELAQELLATIPL   68 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH-------------------HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCG
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-------------------CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhh
Confidence            34455566667777777777777665544                   24556677777777777777777777776654


Q ss_pred             CCCCCCHhhHHHHHHH-hcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC
Q 040338          169 HGFGLSSMLYATAFSA-RASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS  247 (385)
Q Consensus       169 ~g~~p~~~t~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~  247 (385)
                      .  .|+...+..+... +...++...+...++..++..+                       .+...+..+...+...|+
T Consensus        69 ~--~p~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~P-----------------------~~~~~~~~la~~~~~~g~  123 (176)
T 2r5s_A           69 E--YQDNSYKSLIAKLELHQQAAESPELKRLEQELAANP-----------------------DNFELACELAVQYNQVGR  123 (176)
T ss_dssp             G--GCCHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHST-----------------------TCHHHHHHHHHHHHHTTC
T ss_pred             c--cCChHHHHHHHHHHHHhhcccchHHHHHHHHHHhCC-----------------------CCHHHHHHHHHHHHHccc
Confidence            3  2333222221111 1122233345666666665532                       123445666667777778


Q ss_pred             hhHHHHHHHhccc--CC---hhhHHHHHHHHHhcCCCCchHHHH
Q 040338          248 TQKADLAFELMSR--RN---MISWMVLISAFSQAGVLEKPRFFF  286 (385)
Q Consensus       248 ~~~A~~~~~~m~~--~~---~~~~~~li~~~~~~g~~~~a~~~~  286 (385)
                      +++|+..|++..+  |+   ...+..+...+...|+.++|...|
T Consensus       124 ~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y  167 (176)
T 2r5s_A          124 DEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKY  167 (176)
T ss_dssp             HHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHH
Confidence            8888888877765  32   346677777777777777776554

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.59  E-value=2e-07  Score=71.33  Aligned_cols=118  Identities=9%  Similarity=0.034  Sum_probs=96.2

Q ss_pred             hHHHHHHHHHhcCCCCchHHHH-----HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHH
Q 040338          265 SWMVLISAFSQAGVLEKPRFFF-----FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAK  337 (385)
Q Consensus       265 ~~~~li~~~~~~g~~~~a~~~~-----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~  337 (385)
                      ....+.+.+...+.+.+++++-     .+..+...+...|++++|...|++.....+  ...+..+..+|...|++++|+
T Consensus        11 ~~~~l~~~~~~~~~l~~al~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai   90 (151)
T 3gyz_A           11 ISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAA   90 (151)
T ss_dssp             HHHHHHHHHHTSCCTGGGCCSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHH
Confidence            3455555555566666665444     666777778888999999999999999888  888899999999999999999


Q ss_pred             HHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          338 KLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       338 ~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..|++... .| +...|..+..+|...|++++|...|++.++..+.+
T Consensus        91 ~~~~~al~l~P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~~~~  137 (151)
T 3gyz_A           91 DLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDE  137 (151)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCH
T ss_pred             HHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCH
Confidence            99998876 24 56788999999999999999999999999887754

>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=98.59  E-value=6.4e-07  Score=70.50  Aligned_cols=143  Identities=9%  Similarity=-0.058  Sum_probs=112.5

Q ss_pred             HHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH----------HHHHHHH-H-hcccC
Q 040338          235 GKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF----------FFVSLLS-G-CSHSG  299 (385)
Q Consensus       235 ~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~----------~~~~l~~-~-~~~~~  299 (385)
                      +..+...+...|++++|+..|+...+   .+...+..+...+...|++++|+..+          .+..+.. . +...+
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~   88 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQA   88 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHHHHHHHHHHHHhhc
Confidence            44566778889999999999998875   36678888999999999999999888          1111111 1 11222


Q ss_pred             ChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC---cchHHHHHHHHHhcCChHHHHHHHH
Q 040338          300 PVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT---CVIWGALLGACCSHYNTKLAELVMR  373 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~---~~~~~~li~~~~~~g~~~~a~~~~~  373 (385)
                      ....|...+++..+..+  ...+..+...+...|++++|...|+++.+. |+   ...+..+...+...|+.++|...|+
T Consensus        89 ~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~  168 (176)
T 2r5s_A           89 AESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYR  168 (176)
T ss_dssp             TSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             ccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHH
Confidence            33457888999888777  788888999999999999999999988764 54   4578999999999999999999999


Q ss_pred             HHHh
Q 040338          374 NLLQ  377 (385)
Q Consensus       374 ~~~~  377 (385)
                      +.+.
T Consensus       169 ~al~  172 (176)
T 2r5s_A          169 RQLY  172 (176)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8764

>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=98.58  E-value=6.1e-07  Score=84.71  Aligned_cols=152  Identities=10%  Similarity=-0.099  Sum_probs=91.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|.+.+++..+.. +.+...+..+...|.+.|++++|.+.|++..+.+                   +.+...|.
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~   61 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-------------------PGHPEAVA   61 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-------------------TTCHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHH
Confidence            366777777777776653 2346677777777777788888888777766554                   34566777


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      .+...|...|++++|.+.|++..+.. +-+...+..+..++.+.|++++|.+.+++..+....                 
T Consensus        62 ~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-----------------  123 (568)
T 2vsy_A           62 RLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE-----------------  123 (568)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-----------------
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-----------------
Confidence            77777777888888888887776642 224566777777777778888888887777776431                 


Q ss_pred             CCCCCchhhHHHHHHHHHHcC---CChhHHHHHHHhccc
Q 040338          225 CNGIESSIQIGKALVTMYAEG---GSTQKADLAFELMSR  260 (385)
Q Consensus       225 ~~~~~~~~~~~~~li~~~~~~---g~~~~A~~~~~~m~~  260 (385)
                            +...+..+...+...   |+.++|.+.+++..+
T Consensus       124 ------~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A          124 ------EPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             ------CHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             ------CHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence                  222345555556666   677777777777654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.58  E-value=9.2e-07  Score=71.74  Aligned_cols=160  Identities=8%  Similarity=-0.125  Sum_probs=112.0

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCchHHHh----------------HHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           64 CVGNIKMALHLHGLVKKFYFVSDESIAKS----------------SIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~----------------li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      ..|++++|...|+...+... -+...|..                +..+|.+.|++++|...|++..+.+          
T Consensus        16 ~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----------   84 (208)
T 3urz_A           16 EAGQNGQAVSYFRQTIALNI-DRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA----------   84 (208)
T ss_dssp             HTTCHHHHHHHHHHHHHHCH-HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             HCCCHHHHHHHHHHHHHhCC-CChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC----------
Confidence            37999999999999988642 24556666                8888999999999999998876655          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCc--cchhhHHHHHHHh
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDL--EWGPHLHSRVVHM  204 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~--~~a~~~~~~~~~~  204 (385)
                               +.+...|..+...+...|++++|+..|++..+.  .| +..++..+..++...|+.  ..+...+....  
T Consensus        85 ---------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~--  151 (208)
T 3urz_A           85 ---------PNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS--  151 (208)
T ss_dssp             ---------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC-----
T ss_pred             ---------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh--
Confidence                     357788899999999999999999999999875  45 566777777776555432  33333333332  


Q ss_pred             CCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHH
Q 040338          205 EPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVL  269 (385)
Q Consensus       205 ~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~l  269 (385)
                        .|+...                    ..+.....++...|++++|+..|++..+  |+......+
T Consensus       152 --~~~~~~--------------------~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l  196 (208)
T 3urz_A          152 --SPTKMQ--------------------YARYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTL  196 (208)
T ss_dssp             --CCCHHH--------------------HHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             --CCCchh--------------------HHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHH
Confidence              222221                    1223344556667899999999999876  555444433

>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=98.58  E-value=3.7e-07  Score=69.84  Aligned_cols=137  Identities=8%  Similarity=-0.120  Sum_probs=98.7

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|+..++...... +-+...+-.+...|.+.|++++|++.|++..+.+                   +.+..+|.
T Consensus        10 ~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-------------------p~~~~a~~   69 (150)
T 4ga2_A           10 KADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-------------------ERDPKAHR   69 (150)
T ss_dssp             HHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             cChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHH
Confidence            677888888887776542 2234556677888888899999998888876555                   35677888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhH-HHHHHHhCCCCchHHHHHHHHHHHh
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHL-HSRVVHMEPSLDVFVGSGLIDMYLK  222 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~li~~~~~  222 (385)
                      .+..+|.+.|++++|+..|++..+.  .| +...+..+...+.+.|+.+++.+. ++...+..+ -++.+|......+.+
T Consensus        70 ~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P-~~~~~~~l~~~ll~~  146 (150)
T 4ga2_A           70 FLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFP-GSPAVYKLKEQLLDC  146 (150)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHST-TCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHH
Confidence            8888889999999999999888774  45 466788888888888888776655 477777643 244555544444444


Q ss_pred             cC
Q 040338          223 CG  224 (385)
Q Consensus       223 ~g  224 (385)
                      .|
T Consensus       147 ~G  148 (150)
T 4ga2_A          147 EG  148 (150)
T ss_dssp             CC
T ss_pred             hC
Confidence            44

>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=98.55  E-value=1.1e-06  Score=71.17  Aligned_cols=121  Identities=14%  Similarity=-0.057  Sum_probs=76.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...+++.    +.|+...+..+..+|.+.|++++|...|++..+.+                   +.+...|.
T Consensus        19 ~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------------~~~~~~~~   75 (213)
T 1hh8_A           19 KKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-------------------KHLAVAYF   75 (213)
T ss_dssp             TTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             hCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------ccchHHHH
Confidence            57777777776655    24566666777777777777777777776654433                   24455666


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCC--------------CC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGF--------------GL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL  208 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~--------------~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  208 (385)
                      .+..++...|++++|+..|++..+...              .| ....+..+..++...|++++|...++...+..+..
T Consensus        76 ~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  154 (213)
T 1hh8_A           76 QRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  154 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCccc
Confidence            666777777777777777777665321              11 12455666666777777777777777776655433

>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=98.52  E-value=1.3e-06  Score=82.51  Aligned_cols=150  Identities=6%  Similarity=-0.092  Sum_probs=108.8

Q ss_pred             hhhHHHHHhhhC---CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHH
Q 040338           34 IDDDYRVFCDIG---PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAF  110 (385)
Q Consensus        34 ~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~  110 (385)
                      +++|...|++..   +.+...|..+-..+..   .|++++|.+.+++..+.. +.+...+..+..+|...|++++|.+.|
T Consensus         5 ~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            5 GPRELLQLRAAVRHRPQDFVAWLMLADAELG---MGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             ----------------CCHHHHHHHHHHHHH---HTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            445555555443   2345667777777666   799999999999988864 335778888889999999999999999


Q ss_pred             HhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCc--
Q 040338          111 LRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASV--  188 (385)
Q Consensus       111 ~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~--  188 (385)
                      ++..+.+                   +.+...+..+..++.+.|++++|.+.|++..+.. +-+...+..+..++...  
T Consensus        81 ~~al~~~-------------------p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~  140 (568)
T 2vsy_A           81 QQASDAA-------------------PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCD  140 (568)
T ss_dssp             HHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhcC-------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhc
Confidence            8876544                   3567788888899999999999999999988752 22566777888888888  


Q ss_pred             -cCccchhhHHHHHHHhCCC
Q 040338          189 -YDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       189 -~~~~~a~~~~~~~~~~~~~  207 (385)
                       |+.++|.+.+++..+.+..
T Consensus       141 ~g~~~~A~~~~~~al~~~p~  160 (568)
T 2vsy_A          141 WRALDVLSAQVRAAVAQGVG  160 (568)
T ss_dssp             CTTHHHHHHHHHHHHHHTCC
T ss_pred             cccHHHHHHHHHHHHhcCCc
Confidence             8899999999998887654

>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=98.51  E-value=2.9e-06  Score=68.78  Aligned_cols=125  Identities=10%  Similarity=-0.108  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHh
Q 040338          234 IGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAK  313 (385)
Q Consensus       234 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  313 (385)
                      .+..+...+...|++++|+..|++..+++...+..+...|...|++++|+..+                      ++..+
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~----------------------~~al~   65 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAF----------------------TRSIN   65 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHH----------------------HHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHH----------------------HHHHH
Confidence            45567778889999999999999998777777777777777666666665554                      44433


Q ss_pred             ccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-Cc----------------chHHHHHHHHHhcCChHHHHHHHH
Q 040338          314 FTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TC----------------VIWGALLGACCSHYNTKLAELVMR  373 (385)
Q Consensus       314 ~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~----------------~~~~~li~~~~~~g~~~~a~~~~~  373 (385)
                      ..+  ...+..+..+|...|++++|.+.|++..+. | +.                ..|..+..+|...|++++|...++
T Consensus        66 ~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  145 (213)
T 1hh8_A           66 RDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLA  145 (213)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hCccchHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHH
Confidence            333  444444555555555555555555544331 1 11                344455555555555555555555


Q ss_pred             HHHhccc
Q 040338          374 NLLQLDV  380 (385)
Q Consensus       374 ~~~~~~~  380 (385)
                      +..+..|
T Consensus       146 ~al~~~p  152 (213)
T 1hh8_A          146 LATSMKS  152 (213)
T ss_dssp             HHHTTCC
T ss_pred             HHHHcCc
Confidence            5555444

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.50  E-value=0.00012  Score=62.76  Aligned_cols=230  Identities=8%  Similarity=-0.014  Sum_probs=159.8

Q ss_pred             HHHHHHHHHhhhccC-ChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcC--ChhHHHHHHHhccCCCccccccchHHH
Q 040338           52 YNTMINGGVRCLCVG-NIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCG--AVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        52 ~~~li~~~~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g--~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      |..++.-+......| ..++|+++++.+...+. -+..+|+.--.++...|  +++++++.++.+...+           
T Consensus        32 y~~~~~~~~a~~~~~e~s~~aL~~t~~~L~~nP-~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-----------   99 (306)
T 3dra_A           32 YKQIMGLLLALMKAEEYSERALHITELGINELA-SHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-----------   99 (306)
T ss_dssp             HHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCc-HHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-----------
Confidence            455554444333344 45799999999998752 25566888888888888  9999999999887665           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHH----HhC---CCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCcc--chhhHHH
Q 040338          129 LIMFQKMPERDLVSWNTMISIL----TRH---GFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLE--WGPHLHS  199 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~----~~~---~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~--~a~~~~~  199 (385)
                              +.+..+|+.--..+    ...   +++++++.+++++.+.. +-|.+.++.--..+.+.|.++  ++++.++
T Consensus       100 --------Pk~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~  170 (306)
T 3dra_A          100 --------EKNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVD  170 (306)
T ss_dssp             --------TTCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHH
T ss_pred             --------cccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHH
Confidence                    35666777655554    455   78999999999999852 337777776666666677777  9999999


Q ss_pred             HHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC------hhHHHHHHHhccc---CChhhHHHHH
Q 040338          200 RVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS------TQKADLAFELMSR---RNMISWMVLI  270 (385)
Q Consensus       200 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~------~~~A~~~~~~m~~---~~~~~~~~li  270 (385)
                      .+++..+ -+..                      .|+.-...+.+.|+      ++++++.++...+   .|...|+-+-
T Consensus       171 ~~i~~d~-~N~s----------------------AW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~  227 (306)
T 3dra_A          171 KVIDTDL-KNNS----------------------AWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNYLL  227 (306)
T ss_dssp             HHHHHCT-TCHH----------------------HHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHHHhCC-CCHH----------------------HHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCCCCccHHHHHH
Confidence            9998764 2333                      33443344444444      7888888887765   3778888888


Q ss_pred             HHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhcc---c--hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          271 SAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFT---Y--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       271 ~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ..+.+.|+..+++.                     .+.+++...+   +  +..+..+.+.|.+.|+.++|.++++.+.+
T Consensus       228 ~ll~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          228 GIHERFDRSITQLE---------------------EFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             HHHHHTTCCGGGGH---------------------HHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhcCCChHHHH---------------------HHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            88888887554432                     2222222222   2  66677788888888888899988888765


Q ss_pred             C
Q 040338          346 K  346 (385)
Q Consensus       346 ~  346 (385)
                      +
T Consensus       287 ~  287 (306)
T 3dra_A          287 K  287 (306)
T ss_dssp             T
T ss_pred             c
Confidence            3

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.50  E-value=5.3e-06  Score=68.07  Aligned_cols=157  Identities=10%  Similarity=-0.025  Sum_probs=103.6

Q ss_pred             cCChHHHHHHHHHHHHhccCC--CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCc-c
Q 040338           65 VGNIKMALHLHGLVKKFYFVS--DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDL-V  141 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~-~  141 (385)
                      .|++++|...|+.+.+.....  ....+..+..+|.+.|++++|+..|++..+..+.                 .+.. .
T Consensus        17 ~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~-----------------~~~~~~   79 (225)
T 2yhc_A           17 DGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT-----------------HPNIDY   79 (225)
T ss_dssp             HTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-----------------CTTHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-----------------CCcHHH
Confidence            799999999999999864221  1356778889999999999999999887654420                 1111 1


Q ss_pred             hHHHHHHHHH------------------hCCCchHHHHHHHHHHHCCCCCCHh-hH-----------------HHHHHHh
Q 040338          142 SWNTMISILT------------------RHGFGFETLCTFIELWNHGFGLSSM-LY-----------------ATAFSAR  185 (385)
Q Consensus       142 ~~~~li~~~~------------------~~~~~~~a~~~~~~m~~~g~~p~~~-t~-----------------~~ll~~~  185 (385)
                      .+..+..++.                  ..|++++|+..|+++.+.  .|+.. ..                 ..+...+
T Consensus        80 a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~  157 (225)
T 2yhc_A           80 VMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKRLVFLKDRLAKYEYSVAEYY  157 (225)
T ss_dssp             HHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333443                  357889999999998875  34322 21                 1334456


Q ss_pred             cCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          186 ASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       186 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                      .+.|++++|+..++.+++..+....                    ....+..+..+|.+.|+.++|.+.++.+..
T Consensus       158 ~~~~~~~~A~~~~~~~l~~~p~~~~--------------------~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~  212 (225)
T 2yhc_A          158 TERGAWVAVVNRVEGMLRDYPDTQA--------------------TRDALPLMENAYRQMQMNAQAEKVAKIIAA  212 (225)
T ss_dssp             HHHTCHHHHHHHHHHHHHHSTTSHH--------------------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHcCcHHHHHHHHHHHHHHCcCCCc--------------------cHHHHHHHHHHHHHcCCcHHHHHHHHHHHh
Confidence            6777888888888887776432110                    113445666777777788888888877654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.46  E-value=9.6e-07  Score=65.28  Aligned_cols=97  Identities=9%  Similarity=-0.124  Sum_probs=84.6

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-C-CCcchHHHHHHHHHhc
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-K-PTCVIWGALLGACCSH  362 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~-p~~~~~~~li~~~~~~  362 (385)
                      .+......|.+.|++++|+..|++..+..+  ...+..+..+|.+.|++++|++.|++..+ . .+...|..+..+|...
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~   94 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLVAM   94 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC
Confidence            455666778888999999999999988887  88888999999999999999999998876 2 4567899999999999


Q ss_pred             CChHHHHHHHHHHHhccccCC
Q 040338          363 YNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       363 g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      |++++|.+.|++.++.+|.+.
T Consensus        95 ~~~~~A~~~~~~al~l~P~~~  115 (126)
T 4gco_A           95 REWSKAQRAYEDALQVDPSNE  115 (126)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCH
T ss_pred             CCHHHHHHHHHHHHHHCcCCH
Confidence            999999999999999988753

>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=98.45  E-value=7e-06  Score=70.35  Aligned_cols=142  Identities=9%  Similarity=-0.093  Sum_probs=112.2

Q ss_pred             HHHHHHHHcCCChhHHHHHHHhcccC-----C----hhhHHHHHHHHHhcCCCCchHHHH------------------HH
Q 040338          236 KALVTMYAEGGSTQKADLAFELMSRR-----N----MISWMVLISAFSQAGVLEKPRFFF------------------FF  288 (385)
Q Consensus       236 ~~li~~~~~~g~~~~A~~~~~~m~~~-----~----~~~~~~li~~~~~~g~~~~a~~~~------------------~~  288 (385)
                      ...+..+...|++++|..++++..+.     +    ...+..+...+...|++++|+..+                  ++
T Consensus        79 ~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~  158 (293)
T 3u3w_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIE  158 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHH
Confidence            34467788889999999999887652     1    123334666677778888888887                  58


Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhc-------cc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-------CC-cch
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKF-------TY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-------PT-CVI  351 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-------p~-~~~  351 (385)
                      +.+...|...|++++|...++++.+.       ..  ..++..+...|.+.|++++|.+.+++..+-       +. ..+
T Consensus       159 ~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~  238 (293)
T 3u3w_A          159 NAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHH
Confidence            89999999999999999999998841       11  668888999999999999999999877641       11 457


Q ss_pred             HHHHHHHHHhcCC-hHHHHHHHHHHHh
Q 040338          352 WGALLGACCSHYN-TKLAELVMRNLLQ  377 (385)
Q Consensus       352 ~~~li~~~~~~g~-~~~a~~~~~~~~~  377 (385)
                      |..+..+|.+.|+ +++|...+++...
T Consensus       239 ~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          239 YYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            8899999999995 6999999988764

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.45  E-value=9.3e-07  Score=71.00  Aligned_cols=134  Identities=10%  Similarity=-0.027  Sum_probs=88.4

Q ss_pred             CCChhHHHH---HHHhcccCChhhHHHHHHHHHhcCCCCchHHHH------------------HHHHHHHHhcccCChhh
Q 040338          245 GGSTQKADL---AFELMSRRNMISWMVLISAFSQAGVLEKPRFFF------------------FFVSLLSGCSHSGPVTK  303 (385)
Q Consensus       245 ~g~~~~A~~---~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~l~~~~~~~~~~~~  303 (385)
                      .|++++|.+   .+..-......++..+...+...|++++|+..+                  ++..+...+...|++++
T Consensus         5 ~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~   84 (203)
T 3gw4_A            5 AHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDA   84 (203)
T ss_dssp             --CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             cccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHH
Confidence            455555555   332211112344555555555555555555555                  56666777777788888


Q ss_pred             HHHHHHHHHhc------cc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CC----cchHHHHHHHHHhcCChH
Q 040338          304 GKHYFTAMAKF------TY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PT----CVIWGALLGACCSHYNTK  366 (385)
Q Consensus       304 a~~~~~~~~~~------~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~----~~~~~~li~~~~~~g~~~  366 (385)
                      |...+++....      ..   ...+..+...+...|++++|.+.+++....    ++    ..++..+...+...|+++
T Consensus        85 A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  164 (203)
T 3gw4_A           85 ARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLL  164 (203)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHH
Confidence            88777776654      11   556777888999999999999999877541    22    234678888999999999


Q ss_pred             HHHHHHHHHHhc
Q 040338          367 LAELVMRNLLQL  378 (385)
Q Consensus       367 ~a~~~~~~~~~~  378 (385)
                      +|...+++..+.
T Consensus       165 ~A~~~~~~al~~  176 (203)
T 3gw4_A          165 EAQQHWLRARDI  176 (203)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999887654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.44  E-value=2.5e-06  Score=65.18  Aligned_cols=85  Identities=9%  Similarity=-0.028  Sum_probs=64.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...|+...+.. +.+...|..+..+|.+.|++++|+..|++..+.+                   +.+...|.
T Consensus        49 ~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-------------------P~~~~~~~  108 (151)
T 3gyz_A           49 KGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-------------------KNDYTPVF  108 (151)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------------------SSCCHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-------------------CCCcHHHH
Confidence            788888888888887764 3366777778888888888888888887776554                   34566777


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      .+..+|.+.|++++|...|++..+.
T Consensus       109 ~lg~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          109 HTGQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7888888888888888888887764

>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=98.44  E-value=2.8e-06  Score=64.85  Aligned_cols=133  Identities=7%  Similarity=-0.156  Sum_probs=102.2

Q ss_pred             hhhhHHHHHhhhCCCC---hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHH
Q 040338           33 LIDDDYRVFCDIGPRY---LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESA  109 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~  109 (385)
                      ++++|...|+.....+   ...+-.+-..|..   .|++++|.+.|++..+.. +-+..+|..+..+|.+.|++++|...
T Consensus        12 ~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~---~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~   87 (150)
T 4ga2_A           12 DVERYIASVQGSTPSPRQKSIKGFYFAKLYYE---AKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVEC   87 (150)
T ss_dssp             HHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hHHHHHHHHHHhcccCcccHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHH
Confidence            6777777777665332   3455556666666   899999999999999875 34788999999999999999999999


Q ss_pred             HHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHH-HHHHHHCCCCC-CHhhHHHHHHHhcC
Q 040338          110 FLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCT-FIELWNHGFGL-SSMLYATAFSARAS  187 (385)
Q Consensus       110 ~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~-~~~m~~~g~~p-~~~t~~~ll~~~~~  187 (385)
                      |++..+.+                   +.+..+|..+...|.+.|++++|... +++..+.  .| +...|......+..
T Consensus        88 ~~~al~~~-------------------p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~  146 (150)
T 4ga2_A           88 YRRSVELN-------------------PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDC  146 (150)
T ss_dssp             HHHHHHHC-------------------TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHT
T ss_pred             HHHHHHhC-------------------CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHH
Confidence            99887655                   35678899999999999999887665 5777764  55 55666666666655


Q ss_pred             ccC
Q 040338          188 VYD  190 (385)
Q Consensus       188 ~~~  190 (385)
                      .|+
T Consensus       147 ~G~  149 (150)
T 4ga2_A          147 EGE  149 (150)
T ss_dssp             CCC
T ss_pred             hCc
Confidence            554

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.41  E-value=0.00024  Score=60.81  Aligned_cols=219  Identities=8%  Similarity=-0.066  Sum_probs=151.5

Q ss_pred             hHHHHHHHHHHHHcccchhhHHhhhhhHHHHHhhhC--CC-ChhhHHHHHHHHHhhhccC--ChHHHHHHHHHHHHhccC
Q 040338           10 LPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIG--PR-YLFTYNTMINGGVRCLCVG--NIKMALHLHGLVKKFYFV   84 (385)
Q Consensus        10 ~~~a~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~--~~~~a~~~~~~m~~~g~~   84 (385)
                      +..+...+..+.+.+-       ..++|..+++.+.  .| +...||.=-..+..   .+  ++++++++++.+......
T Consensus        32 y~~~~~~~~a~~~~~e-------~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~---l~~~~~~eeL~~~~~~L~~nPk  101 (306)
T 3dra_A           32 YKQIMGLLLALMKAEE-------YSERALHITELGINELASHYTIWIYRFNILKN---LPNRNLYDELDWCEEIALDNEK  101 (306)
T ss_dssp             HHHHHHHHHHHHHTTC-------CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT---CTTSCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcCC-------CCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHH---cccccHHHHHHHHHHHHHHCcc
Confidence            3445555555555442       2346777777665  34 44556655555444   56  999999999999987543


Q ss_pred             CCchHHHhHHHHH----Hhc---CChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCch
Q 040338           85 SDESIAKSSIDMH----VKC---GAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGF  157 (385)
Q Consensus        85 ~~~~~~~~li~~~----~~~---g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~  157 (385)
                       +..+|+.--..+    ...   +++++++.+++++.+.+                   +.|-.+|+--...+.+.|+++
T Consensus       102 -~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-------------------pkny~aW~~R~~vl~~l~~~~  161 (306)
T 3dra_A          102 -NYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-------------------PKNHHVWSYRKWLVDTFDLHN  161 (306)
T ss_dssp             -CCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCTT
T ss_pred             -cHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHhcccC
Confidence             667777766666    555   78999999999988766                   478888888888888888888


Q ss_pred             --HHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccC------ccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCC--
Q 040338          158 --ETLCTFIELWNHGFGLSSMLYATAFSARASVYD------LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNG--  227 (385)
Q Consensus       158 --~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~------~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~--  227 (385)
                        ++++.++++.+... -|...|+.-...+.+.+.      ++++++.++.++...+ -|...|+-+-..+.+.|...  
T Consensus       162 ~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~~~  239 (306)
T 3dra_A          162 DAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSITQ  239 (306)
T ss_dssp             CHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCGGG
T ss_pred             hHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCChHH
Confidence              99999999988633 366666655555555555      7788888888888754 56667766666666666432  


Q ss_pred             -----------C---CchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          228 -----------I---ESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       228 -----------~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                                 .   ..+...+..+...|.+.|+.++|.++++.+.+
T Consensus       240 ~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          240 LEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             GHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence                       1   33556666777777777777777777777654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.39  E-value=3.5e-06  Score=61.34  Aligned_cols=113  Identities=11%  Similarity=0.023  Sum_probs=87.2

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  166 (385)
                      ...+..+...+...|++++|.+.|+++.+.+                   +.+..++..+...+.+.|++++|..+++++
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~   69 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-------------------PNNAEAWYNLGNAYYKQGDYDEAIEYYQKA   69 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-------------------cCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            4677888888899999999999998876543                   346678888889999999999999999998


Q ss_pred             HHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHH
Q 040338          167 WNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMY  220 (385)
Q Consensus       167 ~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  220 (385)
                      .+.. +.+..++..+...+...|++++|...++.+.+..+ .+...+..+...+
T Consensus        70 ~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~  121 (125)
T 1na0_A           70 LELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAKQNLGNAK  121 (125)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHH
Confidence            8752 33677788888889999999999999999888754 2333443443333

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.39  E-value=5.8e-06  Score=60.13  Aligned_cols=112  Identities=11%  Similarity=0.032  Sum_probs=89.4

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ...|..+...+..   .|++++|.+.++++.+.. +.+..++..+...+.+.|++++|...|+++.+.+           
T Consensus         9 ~~~~~~~~~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-----------   73 (125)
T 1na0_A            9 AEAWYNLGNAYYK---QGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-----------   73 (125)
T ss_dssp             HHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHHHHHHHH---cCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-----------
Confidence            4567777777666   899999999999999874 4467888999999999999999999998876544           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHh
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSAR  185 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~  185 (385)
                              +.+..++..+...+...|++++|...|+++.+.  .| +...+..+...+
T Consensus        74 --------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~  121 (125)
T 1na0_A           74 --------PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--DPNNAEAKQNLGNAK  121 (125)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             --------CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHH
Confidence                    356778899999999999999999999999875  34 344444444333

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.36  E-value=6.5e-06  Score=60.79  Aligned_cols=100  Identities=10%  Similarity=-0.019  Sum_probs=60.2

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +...+..+...+.+.|++++|...|++..+.+                   +.+..++..+...+...|++++|+..+++
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~   75 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-------------------PKDAKLYSNRAACYTKLLEFQLALKDCEE   75 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-------------------TTCHHHHHHHHHHHTTTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------------------CCcHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            34555566666666666666666666655443                   23455566666666666666666666666


Q ss_pred             HHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          166 LWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       166 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      ..+.. +.+...+..+..++.+.|++++|.+.++...+..
T Consensus        76 a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  114 (133)
T 2lni_A           76 CIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLD  114 (133)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            65531 2245555666666666666666666666666553

>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=98.35  E-value=8.6e-06  Score=69.76  Aligned_cols=161  Identities=11%  Similarity=-0.060  Sum_probs=114.6

Q ss_pred             cCChHHHHHHHHHHHHhcc-CCCc----hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC
Q 040338           65 VGNIKMALHLHGLVKKFYF-VSDE----SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD  139 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~-~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~  139 (385)
                      .|++++|..++++..+... .|+.    ..+..+...+...|++++|+..|++..+...               .  .++
T Consensus        88 ~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~---------------~--~~~  150 (293)
T 3u3w_A           88 QKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQL---------------T--GID  150 (293)
T ss_dssp             TTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCC---------------C--CSC
T ss_pred             HhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhc---------------c--ccc
Confidence            8999999999999987421 2221    1334466677777899999999988754221               0  122


Q ss_pred             ----cchHHHHHHHHHhCCCchHHHHHHHHHHH----C-CCCCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCc
Q 040338          140 ----LVSWNTMISILTRHGFGFETLCTFIELWN----H-GFGLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLD  209 (385)
Q Consensus       140 ----~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~-g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  209 (385)
                          ..+|+.+...|...|++++|+..|++..+    . +..|. ..+|..+...|.+.|++++|...+++.++.....+
T Consensus       151 ~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~  230 (293)
T 3u3w_A          151 VYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRIN  230 (293)
T ss_dssp             TTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcC
Confidence                23689999999999999999999999874    1 22232 34788899999999999999999998876421110


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC-hhHHHHHHHhcc
Q 040338          210 VFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS-TQKADLAFELMS  259 (385)
Q Consensus       210 ~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~-~~~A~~~~~~m~  259 (385)
                      .                 ...-..+|..+...|.+.|+ .++|.+.|++..
T Consensus       231 ~-----------------~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          231 S-----------------MALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             B-----------------CTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             c-----------------HHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            0                 01123456778888888885 588888887665

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.34  E-value=1.7e-06  Score=69.39  Aligned_cols=162  Identities=9%  Similarity=-0.096  Sum_probs=114.6

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC--CCcch
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE--RDLVS  142 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~--~~~~~  142 (385)
                      .|++++|.++++.+.. .......++..+...+...|++++|...+++..               .++.+...  ....+
T Consensus         5 ~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al---------------~~~~~~~~~~~~~~~   68 (203)
T 3gw4_A            5 AHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQ---------------QQAQKSGDHTAEHRA   68 (203)
T ss_dssp             --CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------HHHHTTCCHHHHHHH
T ss_pred             cccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHH---------------HHHHHcCCcHHHHHH
Confidence            6999999996655543 222356788889999999999999999986643               33333322  23557


Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHC----CCCC--CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC-CchHHHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNH----GFGL--SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS-LDVFVGSG  215 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  215 (385)
                      ++.+...+...|++++|...+++..+.    +-.|  ....+..+...+...|++++|...+++..+.... .+..    
T Consensus        69 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~----  144 (203)
T 3gw4_A           69 LHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQV----  144 (203)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHH----
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchH----
Confidence            888889999999999999999887653    2122  2345777888899999999999999988754211 1111    


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                                    .-..++..+...+...|++++|...+++..+
T Consensus       145 --------------~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          145 --------------AIACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             --------------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                          1123456778888899999999999887754

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.34  E-value=3.7e-06  Score=72.08  Aligned_cols=144  Identities=9%  Similarity=-0.117  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHcCCChhHHHHHHHhccc--CC-------hhhHHHHHHHHHhcCCCCchHHHH------------------
Q 040338          234 IGKALVTMYAEGGSTQKADLAFELMSR--RN-------MISWMVLISAFSQAGVLEKPRFFF------------------  286 (385)
Q Consensus       234 ~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-------~~~~~~li~~~~~~g~~~~a~~~~------------------  286 (385)
                      .+...+..+...|++++|.+.+++..+  +.       ...+..+...+...|++++|+..+                  
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            445567778888999999998876654  11       123344566677788888888876                  


Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhc---cc------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-------Cc
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKF---TY------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-------TC  349 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-------~~  349 (385)
                      +|+.+...|...|++++|...+++..+.   ..      ..++..+...|.+.|++++|.+.+++..+- +       -.
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            7888899999999999999999998732   11      268888999999999999999999877541 1       14


Q ss_pred             chHHHHHHHHHhcCChHHH-HHHHHHHHh
Q 040338          350 VIWGALLGACCSHYNTKLA-ELVMRNLLQ  377 (385)
Q Consensus       350 ~~~~~li~~~~~~g~~~~a-~~~~~~~~~  377 (385)
                      .+|..+...|.+.|++++| ...+++...
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            5788899999999999999 777877653

>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=98.33  E-value=9.4e-06  Score=62.58  Aligned_cols=130  Identities=8%  Similarity=-0.070  Sum_probs=100.9

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ..|..+-..+..   .|++++|...++...+.. +.+..++..+..++...|++++|...+++..+.+            
T Consensus        14 ~~~~~~a~~~~~---~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~------------   77 (166)
T 1a17_A           14 EELKTQANDYFK---AKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD------------   77 (166)
T ss_dssp             HHHHHHHHHHHH---TTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHH---ccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC------------
Confidence            345555555555   899999999999998874 3467888999999999999999999998876544            


Q ss_pred             HHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhH--HHHHHHhcCccCccchhhHHHHHHH
Q 040338          130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLY--ATAFSARASVYDLEWGPHLHSRVVH  203 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~--~~ll~~~~~~~~~~~a~~~~~~~~~  203 (385)
                             +.+..+|..+..++...|++++|...|++..+... .+...+  ......+...|++++|...+.....
T Consensus        78 -------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           78 -------KKYIKGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             -------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -------cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence                   35677888999999999999999999999987532 234444  3344447778999999988887654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.30  E-value=5.6e-06  Score=60.80  Aligned_cols=97  Identities=9%  Similarity=-0.029  Sum_probs=48.9

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      ..+..+...+...|++++|...|++..+..                   +.+...+..+...+...|++++|...+++..
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~   73 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELN-------------------PANAVYFCNRAAAYSKLGNYAGAVQDCERAI   73 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcC-------------------CCCHHHHHHHHHHHHHhhchHHHHHHHHHHH
Confidence            344445555555555555555555443322                   2234445555555555555555555555554


Q ss_pred             HCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          168 NHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       168 ~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      +.. +.+...+..+...+...|++++|...++...+.
T Consensus        74 ~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  109 (131)
T 2vyi_A           74 CID-PAYSKAYGRMGLALSSLNKHVEAVAYYKKALEL  109 (131)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hcC-ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            431 123444455555555555555555555555554

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.29  E-value=4.4e-05  Score=65.28  Aligned_cols=173  Identities=10%  Similarity=-0.070  Sum_probs=118.3

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC-----chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchH
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD-----ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGII  126 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  126 (385)
                      +...+..+..   .|++++|.+.+....+.....+     ...+..+...+...|++++|+..+++..+...        
T Consensus        78 l~~~~~~~~~---~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~--------  146 (293)
T 2qfc_A           78 FKDQVIMLCK---QKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQL--------  146 (293)
T ss_dssp             HHHHHHHHHH---TTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCC--------
T ss_pred             HHHHHHHHHH---hhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh--------
Confidence            3344445444   8999999999998887532211     12234456667788999999999987654321        


Q ss_pred             HHHHHhcCCCCCC--cchHHHHHHHHHhCCCchHHHHHHHHHHHC-CCCCC-----HhhHHHHHHHhcCccCccchhhHH
Q 040338          127 RLLIMFQKMPERD--LVSWNTMISILTRHGFGFETLCTFIELWNH-GFGLS-----SMLYATAFSARASVYDLEWGPHLH  198 (385)
Q Consensus       127 ~a~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~-----~~t~~~ll~~~~~~~~~~~a~~~~  198 (385)
                             ....+.  ..+|+.+...|...|++++|+..|++..+. ...|+     ..++..+...|.+.|++++|...+
T Consensus       147 -------~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~  219 (293)
T 2qfc_A          147 -------TGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQV  219 (293)
T ss_dssp             -------CSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             -------cCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHH
Confidence                   000122  448889999999999999999999998732 01222     258888999999999999999999


Q ss_pred             HHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHH-HHHHHhcc
Q 040338          199 SRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKA-DLAFELMS  259 (385)
Q Consensus       199 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A-~~~~~~m~  259 (385)
                      ++.++.....+.                 ...-..+|..+...|.+.|+.++| ...+++..
T Consensus       220 ~kal~~~~~~~~-----------------~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          220 NKAIEISCRINS-----------------MALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHTTB-----------------CSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCc-----------------HHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            998764211000                 011234567778888888899998 66676554

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.29  E-value=3.2e-06  Score=60.32  Aligned_cols=96  Identities=13%  Similarity=-0.033  Sum_probs=83.0

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C---CcchHHHHHHHHHh
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P---TCVIWGALLGACCS  361 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p---~~~~~~~li~~~~~  361 (385)
                      +..+...+...|++++|...+++..+..+  ...+..+...+...|++++|.+.|++..+. |   +...|..+...|..
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~~   88 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALRY   88 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHHH
Confidence            34456677788999999999999888776  777888999999999999999999988764 4   46788999999999


Q ss_pred             c-CChHHHHHHHHHHHhccccCC
Q 040338          362 H-YNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       362 ~-g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      . |++++|.+.+++..+..|.++
T Consensus        89 ~~~~~~~A~~~~~~~~~~~p~~~  111 (112)
T 2kck_A           89 IEGKEVEAEIAEARAKLEHHHHH  111 (112)
T ss_dssp             CSSCSHHHHHHHHHHGGGCCCCC
T ss_pred             HhCCHHHHHHHHHHHhhcccCCC
Confidence            9 999999999999999988765

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.29  E-value=6.5e-06  Score=58.62  Aligned_cols=101  Identities=9%  Similarity=-0.093  Sum_probs=65.6

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +...+..+...+.+.|++++|...|++..+.+                   +.+...|..+...+...|++++|...|++
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-------------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~   65 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-------------------PEESKYWLMKGKALYNLERYEEAVDCYNY   65 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-------------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-------------------cCCHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            34556666667777777777777776654433                   23455666667777777777777777777


Q ss_pred             HHHCCCCC--CHhhHHHHHHHhcCc-cCccchhhHHHHHHHhCC
Q 040338          166 LWNHGFGL--SSMLYATAFSARASV-YDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       166 m~~~g~~p--~~~t~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~  206 (385)
                      ..+.. +.  +...+..+..++... |++++|.+.++...+..+
T Consensus        66 a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~p  108 (112)
T 2kck_A           66 VINVI-EDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKLEHH  108 (112)
T ss_dssp             HHHTS-CCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGGCC
T ss_pred             HHHhC-cccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhccc
Confidence            76642 12  355666667777777 777777777777766644

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.28  E-value=1.4e-05  Score=58.61  Aligned_cols=119  Identities=13%  Similarity=0.013  Sum_probs=94.1

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ...|..+...+..   .|++++|...++...+.. +.+...+..+..++...|++++|...+++..+.+           
T Consensus        12 ~~~~~~~~~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-----------   76 (131)
T 2vyi_A           12 AERLKTEGNEQMK---VENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-----------   76 (131)
T ss_dssp             HHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----------
T ss_pred             hHHHHHHHHHHHH---ccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-----------
Confidence            4455666666555   899999999999998864 3467888999999999999999999998876544           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCc
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDL  191 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  191 (385)
                              +.+...+..+...+...|++++|...|++..+.. +.+...+..+..++.+.|++
T Consensus        77 --------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           77 --------PAYSKAYGRMGLALSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             --------ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence                    3567788899999999999999999999998752 22556666777777666654

>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=98.27  E-value=6.5e-06  Score=63.51  Aligned_cols=132  Identities=9%  Similarity=-0.054  Sum_probs=99.2

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  166 (385)
                      ...+..+...+...|++++|...|++..+.+                   +.+..++..+...+...|++++|...+++.
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-------------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a   73 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN-------------------PSNAIYYGNRSLAYLRTECYGYALGDATRA   73 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------------------CCChHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4557777888889999999999998876544                   356778888999999999999999999998


Q ss_pred             HHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCC
Q 040338          167 WNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGG  246 (385)
Q Consensus       167 ~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g  246 (385)
                      .+.. +.+...+..+..++...|++++|...++...+..+. +...+                    .+-.....+.+.|
T Consensus        74 ~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p~-~~~~~--------------------~~~~~~~~~~~~~  131 (166)
T 1a17_A           74 IELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKVKPH-DKDAK--------------------MKYQECNKIVKQK  131 (166)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHH--------------------HHHHHHHHHHHHH
T ss_pred             HHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-CHHHH--------------------HHHHHHHHHHHHH
Confidence            8752 335677888888899999999999999999887542 22222                    1122233355667


Q ss_pred             ChhHHHHHHHhcc
Q 040338          247 STQKADLAFELMS  259 (385)
Q Consensus       247 ~~~~A~~~~~~m~  259 (385)
                      ++++|+..+....
T Consensus       132 ~~~~A~~~~~~~~  144 (166)
T 1a17_A          132 AFERAIAGDEHKR  144 (166)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHcccchH
Confidence            8888888887654

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.27  E-value=1.9e-05  Score=58.13  Aligned_cols=116  Identities=8%  Similarity=-0.050  Sum_probs=92.7

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      .+...|..+...+.+.|++++|...|++..+.. +.+...+..+..++...|++++|.+.++...+....          
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~----------   82 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT----------   82 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT----------
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC----------
Confidence            456678889999999999999999999998752 236778888999999999999999999999887532          


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcC
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAG  277 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g  277 (385)
                                   +...+..+...+.+.|++++|...|++..+  | +...+..+...+...|
T Consensus        83 -------------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           83 -------------FIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             -------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHT
T ss_pred             -------------chHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhc
Confidence                         234456777788888999999999998865  3 4466666777766654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.25  E-value=1.8e-05  Score=58.26  Aligned_cols=84  Identities=7%  Similarity=-0.074  Sum_probs=52.1

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|++.|++..+.. +.+..+|..+..+|.+.|++++|+..|++..+.+                   +.+...|.
T Consensus        26 ~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~a~~   85 (126)
T 4gco_A           26 KGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-------------------SKFIKGYI   85 (126)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-------------------hhhhHHHH
Confidence            566666666666666553 2355666666666666666666666666554433                   24455666


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      .+..++...|++++|+..|++..+
T Consensus        86 ~lg~~~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           86 RKAACLVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            666666666666666666666655

>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=98.25  E-value=2.2e-06  Score=75.11  Aligned_cols=147  Identities=7%  Similarity=-0.134  Sum_probs=115.5

Q ss_pred             hhhhHHHHHhhhC--CC-ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC--------------chHHHhHHH
Q 040338           33 LIDDDYRVFCDIG--PR-YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD--------------ESIAKSSID   95 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~--------------~~~~~~li~   95 (385)
                      ++++|...|+...  .| +...|..+-..+..   .|++++|...|++..+......              ..+|..+..
T Consensus       128 ~~~~A~~~~~~a~~~~p~~a~~~~~~g~~~~~---~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~  204 (336)
T 1p5q_A          128 SFEKAKESWEMNSEEKLEQSTIVKERGTVYFK---EGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAM  204 (336)
T ss_dssp             EEECCCCGGGCCHHHHHHHHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHH
T ss_pred             ecccccchhcCCHHHHHHHHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHH
Confidence            6666766666543  22 34566666666555   8999999999999998743221              488999999


Q ss_pred             HHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-C
Q 040338           96 MHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-S  174 (385)
Q Consensus        96 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~  174 (385)
                      +|.+.|++++|+..|++..+.+                   +.+...|..+..+|...|++++|+..|++..+.  .| +
T Consensus       205 ~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~  263 (336)
T 1p5q_A          205 CHLKLQAFSAAIESCNKALELD-------------------SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNN  263 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSC
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-------------------CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCC
Confidence            9999999999999998876655                   457788999999999999999999999999885  44 5


Q ss_pred             HhhHHHHHHHhcCccCccch-hhHHHHHHH
Q 040338          175 SMLYATAFSARASVYDLEWG-PHLHSRVVH  203 (385)
Q Consensus       175 ~~t~~~ll~~~~~~~~~~~a-~~~~~~~~~  203 (385)
                      ...+..+..++.+.|+.+++ ...++.|..
T Consensus       264 ~~a~~~l~~~~~~~~~~~~a~~~~~~~~~~  293 (336)
T 1p5q_A          264 KAAKTQLAVCQQRIRRQLAREKKLYANMFE  293 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67788888889999999888 456666654

>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=98.25  E-value=3e-06  Score=66.55  Aligned_cols=118  Identities=10%  Similarity=0.075  Sum_probs=63.3

Q ss_pred             HcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--h
Q 040338          243 AEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T  317 (385)
Q Consensus       243 ~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~  317 (385)
                      ...|++++|+..++...+  | +...+..+...|..                      .|++++|...+++..+..+  .
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~----------------------~~~~~~A~~~~~~al~~~p~~~   78 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLW----------------------QNDYSNSLLAYRQALQLRGENA   78 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHH----------------------TTCHHHHHHHHHHHHHHHCSCH
T ss_pred             hhccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH----------------------cCCHHHHHHHHHHHHHcCCCCH
Confidence            345566666666665543  2 33444445555544                      4555555555555555544  4


Q ss_pred             hhHHHHHHH-HHccCCH--HHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          318 CYFVCMVDL-LGLSGLL--GEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       318 ~~~~~li~~-~~~~g~~--~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..+..+..+ +...|++  ++|.+.|++.... | +...+..+...|...|++++|...++++.+..|.+
T Consensus        79 ~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~  148 (177)
T 2e2e_A           79 ELYAALATVLYYQASQHMTAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPR  148 (177)
T ss_dssp             HHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTT
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCC
Confidence            445555555 5556665  6666666655442 3 34455556666666666666666666666665544

>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=98.24  E-value=4e-06  Score=63.85  Aligned_cols=95  Identities=13%  Similarity=-0.064  Sum_probs=67.4

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g  363 (385)
                      +..+...+...|++++|...|+......+  ...+..+..+|...|++++|++.|++.... | +...|..+..+|...|
T Consensus        24 ~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g  103 (148)
T 2vgx_A           24 LYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECLLQXG  103 (148)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcC
Confidence            33444555566677777777777776666  666777777788888888888888776542 3 4566777777888888


Q ss_pred             ChHHHHHHHHHHHhccccC
Q 040338          364 NTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~  382 (385)
                      ++++|...|++.++..|.+
T Consensus       104 ~~~~A~~~~~~al~~~p~~  122 (148)
T 2vgx_A          104 ELAEAESGLFLAQELIANX  122 (148)
T ss_dssp             CHHHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHHCcCC
Confidence            8888888888877766653

>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=98.23  E-value=2.7e-06  Score=62.94  Aligned_cols=96  Identities=7%  Similarity=-0.063  Sum_probs=79.9

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC--------cchHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT--------CVIWGAL  355 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~--------~~~~~~l  355 (385)
                      ++..+...+.+.|++++|+..|++..+..+  ...+..+..+|.+.|++++|++.+++..+. |+        ..+|..+
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~l   89 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRA   89 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHH
Confidence            456677888889999999999999988877  788888999999999999999999887652 21        2367778


Q ss_pred             HHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          356 LGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       356 i~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..++...|++++|++.|++.++..+.|
T Consensus        90 g~~~~~~~~~~~A~~~~~kal~~~~~~  116 (127)
T 4gcn_A           90 GNAFQKQNDLSLAVQWFHRSLSEFRDP  116 (127)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSCCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCcCH
Confidence            888999999999999999988766554

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.22  E-value=4.3e-06  Score=63.09  Aligned_cols=95  Identities=13%  Similarity=-0.065  Sum_probs=73.3

Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCC
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYN  364 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~  364 (385)
                      ..+...+...|++++|...|+......+  ...+..+..+|.+.|++++|+..|++.... | +...|..+..+|...|+
T Consensus        22 ~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~  101 (142)
T 2xcb_A           22 YALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQLGD  101 (142)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCC
Confidence            3445556667778888888888877777  777778888888888888888888877652 3 45667788888888888


Q ss_pred             hHHHHHHHHHHHhccccCC
Q 040338          365 TKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       365 ~~~a~~~~~~~~~~~~~~~  383 (385)
                      +++|...+++..+..|.++
T Consensus       102 ~~~A~~~~~~al~~~p~~~  120 (142)
T 2xcb_A          102 LDGAESGFYSARALAAAQP  120 (142)
T ss_dssp             HHHHHHHHHHHHHHHHTCG
T ss_pred             HHHHHHHHHHHHHhCCCCc
Confidence            8888888888888776543

>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=98.21  E-value=5e-06  Score=65.24  Aligned_cols=120  Identities=7%  Similarity=-0.082  Sum_probs=82.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...++...+.. +.+...+..+...|...|++++|...|++..+.+                   +.+...+.
T Consensus        23 ~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~~~~   82 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-------------------GENAELYA   82 (177)
T ss_dssp             ----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-------------------CSCHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------------------CCCHHHHH
Confidence            577777777777777654 3356777777788888888888888887765443                   24555666


Q ss_pred             HHHHH-HHhCCCc--hHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          145 TMISI-LTRHGFG--FETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       145 ~li~~-~~~~~~~--~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      .+..+ +...|++  ++|...|++..+.  .| +...+..+...+...|++++|...++...+..+
T Consensus        83 ~la~~l~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p  146 (177)
T 2e2e_A           83 ALATVLYYQASQHMTAQTRAMIDKALAL--DSNEITALMLLASDAFMQANYAQAIELWQKVMDLNS  146 (177)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCC
Confidence            66666 6677777  8888888877764  33 456666777777788888888888888777654

>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=98.19  E-value=2e-05  Score=63.93  Aligned_cols=128  Identities=9%  Similarity=0.011  Sum_probs=111.2

Q ss_pred             HHHHHHHhccc-CChhhHHHHHHHHHhcCCCCchHHHH----------HHHHHHHHhcccC----ChhhHHHHHHHHHhc
Q 040338          250 KADLAFELMSR-RNMISWMVLISAFSQAGVLEKPRFFF----------FFVSLLSGCSHSG----PVTKGKHYFTAMAKF  314 (385)
Q Consensus       250 ~A~~~~~~m~~-~~~~~~~~li~~~~~~g~~~~a~~~~----------~~~~l~~~~~~~~----~~~~a~~~~~~~~~~  314 (385)
                      +|+..|++..+ .+...+..|...|...+++++|+..|          ++..+...|.. +    +.++|.+.|++..+.
T Consensus         4 eA~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~   82 (212)
T 3rjv_A            4 EPGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEA   82 (212)
T ss_dssp             CTTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHC
Confidence            45666666655 47788889999999999999999999          77778888887 6    899999999999988


Q ss_pred             cchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCCCC----cchHHHHHHHHHh----cCChHHHHHHHHHHHhc
Q 040338          315 TYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSKPT----CVIWGALLGACCS----HYNTKLAELVMRNLLQL  378 (385)
Q Consensus       315 ~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~----~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~  378 (385)
                      +.+..+..|...|..    .+++++|.+.|++..+..+    ...+..|...|..    .+++++|..++++..+.
T Consensus        83 g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~  158 (212)
T 3rjv_A           83 GSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL  158 (212)
T ss_dssp             TCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc
Confidence            888888888888887    8999999999999988644    7889999999998    88999999999999887

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.17  E-value=7.1e-06  Score=63.54  Aligned_cols=96  Identities=14%  Similarity=0.013  Sum_probs=63.0

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g  363 (385)
                      +..+...+...|++++|...|++..+..+  ...+..+..+|.+.|++++|+..|++.... | +...|..+..+|...|
T Consensus        14 ~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g   93 (164)
T 3sz7_A           14 LKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLARFDMA   93 (164)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcc
Confidence            44455555666666777777777666655  666666677777777777777777666542 3 3556666777777777


Q ss_pred             ChHHHHHHHHHHHhccccCC
Q 040338          364 NTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ++++|...+++.++..|.+.
T Consensus        94 ~~~~A~~~~~~al~~~p~~~  113 (164)
T 3sz7_A           94 DYKGAKEAYEKGIEAEGNGG  113 (164)
T ss_dssp             CHHHHHHHHHHHHHHHSSSC
T ss_pred             CHHHHHHHHHHHHHhCCCch
Confidence            77777777777776666543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.15  E-value=3e-05  Score=58.35  Aligned_cols=85  Identities=8%  Similarity=-0.173  Sum_probs=73.4

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...|+...+.. +.+...|..+..+|.+.|++++|...|++..+.+                   +.+...|.
T Consensus        31 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~   90 (142)
T 2xcb_A           31 AGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-------------------INEPRFPF   90 (142)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCTHHHH
T ss_pred             HccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-------------------CCCcHHHH
Confidence            899999999999998875 3477888889999999999999999998876655                   35677888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      .+..++...|++++|...|+...+.
T Consensus        91 ~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           91 HAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            8999999999999999999998764

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.15  E-value=5e-06  Score=60.86  Aligned_cols=94  Identities=12%  Similarity=-0.041  Sum_probs=77.4

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCCh
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNT  365 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~  365 (385)
                      .+...+.+.|++++|...+++..+..+  ...+..+..++...|++++|+..|++..+. | +...+..+..+|...|++
T Consensus        22 ~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~g~~  101 (121)
T 1hxi_A           22 EEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNA  101 (121)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCH
Confidence            345566788999999999999998887  888888999999999999999999988763 5 566888999999999999


Q ss_pred             HHHHHHHHHHHhccccCC
Q 040338          366 KLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~~  383 (385)
                      ++|...+++.++.+|..+
T Consensus       102 ~~A~~~~~~al~~~P~~~  119 (121)
T 1hxi_A          102 NAALASLRAWLLSQPQYE  119 (121)
T ss_dssp             HHHHHHHHHHHC------
T ss_pred             HHHHHHHHHHHHhCcCCC
Confidence            999999999999888654

>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=98.15  E-value=3.6e-05  Score=58.46  Aligned_cols=96  Identities=9%  Similarity=-0.119  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHH
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLI  130 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~  130 (385)
                      .+..+-..+..   .|++++|...|+...+.. +.+...|..+..+|...|++++|+..|++....+             
T Consensus        23 ~~~~~g~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-------------   85 (148)
T 2vgx_A           23 QLYSLAFNQYQ---SGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-------------   85 (148)
T ss_dssp             HHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------------
T ss_pred             HHHHHHHHHHH---cCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-------------
Confidence            44444445444   899999999999998864 3477888888899999999999999998876554             


Q ss_pred             HhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          131 MFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       131 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                            +.+...|..+..+|...|++++|...|++..+.
T Consensus        86 ------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           86 ------IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             ------TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ------CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence                  356678888889999999999999999988764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.13  E-value=0.00016  Score=65.31  Aligned_cols=197  Identities=9%  Similarity=-0.105  Sum_probs=128.9

Q ss_pred             HHHHHhcCChhHHHHHHHhccCCCccccc-----cchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338           94 IDMHVKCGAVDYAESAFLRMLNPSLFCWK-----FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus        94 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      ...+.+.|++++|++.|.++.+.......     +.......       .....+..+...|...|++++|.+.+..+..
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-------~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~   83 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRN-------EQETSILELGQLYVTMGAKDKLREFIPHSTE   83 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHH-------HHHHHHHHHHHHHHHHTCHHHHHHHHHHTHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhh-------hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45567889999999999887553320000     00000000       0012367788999999999999999988765


Q ss_pred             CC-CCCCH----hhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHH
Q 040338          169 HG-FGLSS----MLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYA  243 (385)
Q Consensus       169 ~g-~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~  243 (385)
                      .- -.++.    .+.+.+-..+...|+.+.+..+++.......               +.++  ...-..++..+...|.
T Consensus        84 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---------------~~~~--~~~~~~~~~~la~~~~  146 (434)
T 4b4t_Q           84 YMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAK---------------REKR--VFLKHSLSIKLATLHY  146 (434)
T ss_dssp             HHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHH---------------HSSC--CSSHHHHHHHHHHHHH
T ss_pred             HHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH---------------HhCc--cHHHHHHHHHHHHHHH
Confidence            31 11222    2233344455667888999988887765311               1100  0112345567778888


Q ss_pred             cCCChhHHHHHHHhccc--------C-ChhhHHHHHHHHHhcCCCCchHHHH-------------------HHHHHHHHh
Q 040338          244 EGGSTQKADLAFELMSR--------R-NMISWMVLISAFSQAGVLEKPRFFF-------------------FFVSLLSGC  295 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~--------~-~~~~~~~li~~~~~~g~~~~a~~~~-------------------~~~~l~~~~  295 (385)
                      ..|++++|..+++....        + ...++..++..|...|++++|...+                   .+..+...+
T Consensus       147 ~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~  226 (434)
T 4b4t_Q          147 QKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILH  226 (434)
T ss_dssp             HHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHT
T ss_pred             HccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHH
Confidence            88899999999887653        1 2357778888888999998888877                   566777788


Q ss_pred             cccCChhhHHHHHHHHHhc
Q 040338          296 SHSGPVTKGKHYFTAMAKF  314 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~  314 (385)
                      ...+++++|...|.+....
T Consensus       227 ~~~~~y~~A~~~~~~a~~~  245 (434)
T 4b4t_Q          227 CEDKDYKTAFSYFFESFES  245 (434)
T ss_dssp             TSSSCHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHH
Confidence            8889999998888777654

>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=98.13  E-value=1.2e-05  Score=57.75  Aligned_cols=95  Identities=8%  Similarity=-0.064  Sum_probs=80.6

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g  363 (385)
                      +..+...+...|++++|...++......+  ...+..+...+...|++++|...+++.... | +...+..+..+|...|
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~   86 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLN   86 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHh
Confidence            45566777788999999999999888776  777888889999999999999999887653 4 5667888999999999


Q ss_pred             ChHHHHHHHHHHHhccccC
Q 040338          364 NTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~  382 (385)
                      ++++|...+++..+.+|.+
T Consensus        87 ~~~~A~~~~~~~~~~~~~~  105 (118)
T 1elw_A           87 RFEEAKRTYEEGLKHEANN  105 (118)
T ss_dssp             CHHHHHHHHHHHHTTCTTC
T ss_pred             hHHHHHHHHHHHHHcCCCC
Confidence            9999999999999887764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.12  E-value=3.3e-05  Score=69.94  Aligned_cols=179  Identities=8%  Similarity=-0.137  Sum_probs=126.7

Q ss_pred             HHHHhCCCchHHHHHHHHHHHCCCCC-CH---------------hhHHHHHHHhcCccCccchhhHHHHHHHhCCC-Cch
Q 040338          148 SILTRHGFGFETLCTFIELWNHGFGL-SS---------------MLYATAFSARASVYDLEWGPHLHSRVVHMEPS-LDV  210 (385)
Q Consensus       148 ~~~~~~~~~~~a~~~~~~m~~~g~~p-~~---------------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~  210 (385)
                      ..+.+.|++++|++.|....+..... +.               ..+..+...|...|++++|.+.+..+...-.. ++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            45678899999999999998753221 11               23677889999999999999999887764211 111


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----CC----hhhHHHHHHHHHhcCCCCc
Q 040338          211 FVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----RN----MISWMVLISAFSQAGVLEK  281 (385)
Q Consensus       211 ~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~g~~~~  281 (385)
                      .+-                  ..+.+.+...+...|+.+.|..+++....     .+    ..++..+...|...|++++
T Consensus        92 ~~~------------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  153 (434)
T 4b4t_Q           92 KTV------------------KVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKD  153 (434)
T ss_dssp             HHH------------------HHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHH------------------HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHH
Confidence            111                  11223344445567889999999887653     11    2467778888889999999


Q ss_pred             hHHHH------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc---------hhhHHHHHHHHHccCCHH
Q 040338          282 PRFFF------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY---------TCYFVCMVDLLGLSGLLG  334 (385)
Q Consensus       282 a~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---------~~~~~~li~~~~~~g~~~  334 (385)
                      |..++                  ++..++..|...|++++|..++++......         ...+..+...+...|+++
T Consensus       154 A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~  233 (434)
T 4b4t_Q          154 SLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYK  233 (434)
T ss_dssp             HHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHH
T ss_pred             HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHH
Confidence            88887                  788888888888999888888887765432         345566667777788888


Q ss_pred             HHHHHHHhCC
Q 040338          335 EAKKLIDEMP  344 (385)
Q Consensus       335 ~A~~~~~~m~  344 (385)
                      +|.+.|.+..
T Consensus       234 ~A~~~~~~a~  243 (434)
T 4b4t_Q          234 TAFSYFFESF  243 (434)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            8877776553

>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=98.12  E-value=8.8e-06  Score=59.78  Aligned_cols=92  Identities=12%  Similarity=-0.126  Sum_probs=80.6

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g  363 (385)
                      +......+...|++++|...|++..+..+  ...+..+..+|.+.|++++|+..+++..+. | +...|..+..+|...|
T Consensus         7 ~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~   86 (126)
T 3upv_A            7 ARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVK   86 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHh
Confidence            45566777888999999999999988877  788889999999999999999999988763 4 5668889999999999


Q ss_pred             ChHHHHHHHHHHHhcc
Q 040338          364 NTKLAELVMRNLLQLD  379 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~  379 (385)
                      ++++|...+++..+.+
T Consensus        87 ~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           87 EYASALETLDAARTKD  102 (126)
T ss_dssp             CHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC
Confidence            9999999999999887

>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=98.08  E-value=0.0037  Score=54.26  Aligned_cols=218  Identities=11%  Similarity=-0.015  Sum_probs=152.9

Q ss_pred             hHHHHHHHHHHHHcccchhhHHhhhhhHHHHHhhhC--CC-ChhhHHHHHHHHHhhhccC-ChHHHHHHHHHHHHhccCC
Q 040338           10 LPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIG--PR-YLFTYNTMINGGVRCLCVG-NIKMALHLHGLVKKFYFVS   85 (385)
Q Consensus        10 ~~~a~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~-~~~~a~~~~~~m~~~g~~~   85 (385)
                      +..+...+..+++.+-       ..++|..+++.+.  .| +...|+.--..+..   .+ .+++++++++.+.+... -
T Consensus        53 y~~~~~~~r~~~~~~e-------~se~AL~lt~~~L~~nP~~ytaWn~R~~iL~~---l~~~l~eEL~~~~~~L~~nP-K  121 (349)
T 3q7a_A           53 YKDAMDYFRAIAAKEE-------KSERALELTEIIVRMNPAHYTVWQYRFSLLTS---LNKSLEDELRLMNEFAVQNL-K  121 (349)
T ss_dssp             HHHHHHHHHHHHHTTC-------CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---TTCCHHHHHHHHHHHHHTTC-C
T ss_pred             HHHHHHHHHHHHHhCC-------CCHHHHHHHHHHHHhCchhHHHHHHHHHHHHH---hhhhHHHHHHHHHHHHHhCC-C
Confidence            3445555555555442       2346777777665  33 45566655444444   56 69999999999998753 3


Q ss_pred             CchHHHhHHHHHHhc-C-ChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCch------
Q 040338           86 DESIAKSSIDMHVKC-G-AVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGF------  157 (385)
Q Consensus        86 ~~~~~~~li~~~~~~-g-~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~------  157 (385)
                      +..+|+.--.++.+. + +.++++++++++.+.+                   +.|-.+|+--...+.+.|.++      
T Consensus       122 ny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~d-------------------pkNy~AW~~R~wvl~~l~~~~~~~~~~  182 (349)
T 3q7a_A          122 SYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPD-------------------PKNYHTWAYLHWLYSHFSTLGRISEAQ  182 (349)
T ss_dssp             CHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSC-------------------TTCHHHHHHHHHHHHHHHHTTCCCHHH
T ss_pred             cHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHhccccccchhh
Confidence            777888888888776 7 8899999999998877                   467778877666666666666      


Q ss_pred             --HHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccC-------ccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCC--
Q 040338          158 --ETLCTFIELWNHGFGLSSMLYATAFSARASVYD-------LEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCN--  226 (385)
Q Consensus       158 --~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~--  226 (385)
                        ++++.++++.+.. +-|...|+.....+.+.+.       ++++++.++..+...+ -|...|+-+-..+.+.|..  
T Consensus       183 ~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P-~n~SaW~Ylr~Ll~~~~~~~~  260 (349)
T 3q7a_A          183 WGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIP-HNVSAWNYLRGFLKHFSLPLV  260 (349)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCCCcc
Confidence              8899999888763 2367777776666666665       5677777777777643 4666776666666665543  


Q ss_pred             ----------------C--------------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhcc
Q 040338          227 ----------------G--------------------IESSIQIGKALVTMYAEGGSTQKADLAFELMS  259 (385)
Q Consensus       227 ----------------~--------------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  259 (385)
                                      .                    ..++......+.+.|...|+.++|.++++.+.
T Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~  329 (349)
T 3q7a_A          261 PILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLS  329 (349)
T ss_dssp             GGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence                            0                    14667777888888888888888888888876

>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=98.07  E-value=2e-05  Score=57.78  Aligned_cols=64  Identities=9%  Similarity=-0.038  Sum_probs=31.3

Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHh
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHM  204 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  204 (385)
                      +...|..+..++.+.|++++|+..|++..+.  .| +...+..+..++...|++++|...++...+.
T Consensus        37 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           37 DARGYSNRAAALAKLMSFPEAIADCNKAIEK--DPNFVRAYIRKATAQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHHh
Confidence            3444555555555555555555555555443  22 2344444445555555555555555554443

>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=98.05  E-value=0.003  Score=54.76  Aligned_cols=231  Identities=7%  Similarity=-0.034  Sum_probs=151.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcC-ChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCG-AVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      .+..++|+++++.+...+.. +..+|+.--..+...| .+++++++++.+...+                   +.+..+|
T Consensus        67 ~e~se~AL~lt~~~L~~nP~-~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-------------------PKny~aW  126 (349)
T 3q7a_A           67 EEKSERALELTEIIVRMNPA-HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-------------------LKSYQVW  126 (349)
T ss_dssp             TCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-------------------CCCHHHH
T ss_pred             CCCCHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-------------------CCcHHHH
Confidence            55667999999999987532 5567888777887788 5999999999988776                   4677888


Q ss_pred             HHHHHHHHhC-C-CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCcc--------chhhHHHHHHHhCCCCchHHH
Q 040338          144 NTMISILTRH-G-FGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLE--------WGPHLHSRVVHMEPSLDVFVG  213 (385)
Q Consensus       144 ~~li~~~~~~-~-~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~  213 (385)
                      +.--..+.+. + ++++++++++++.+.. +-|...++.-...+.+.+.++        ++++..+.+++..+ -+... 
T Consensus       127 ~hR~wlL~~l~~~~~~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SA-  203 (349)
T 3q7a_A          127 HHRLLLLDRISPQDPVSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSA-  203 (349)
T ss_dssp             HHHHHHHHHHCCSCCHHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHH-
T ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHH-
Confidence            8877777666 6 8999999999998752 236777766555555555666        78888888888754 23334 


Q ss_pred             HHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC-------hhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchH
Q 040338          214 SGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS-------TQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPR  283 (385)
Q Consensus       214 ~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~-------~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~  283 (385)
                                           |+.....+.+.++       ++++++.+++..+  | |...|+-+-..+.+.|+....+
T Consensus       204 ---------------------W~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~  262 (349)
T 3q7a_A          204 ---------------------WGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPI  262 (349)
T ss_dssp             ---------------------HHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGG
T ss_pred             ---------------------HHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccc
Confidence                                 4444444444444       5788888877765  3 6778887777777777652211


Q ss_pred             HHH-----------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC
Q 040338          284 FFF-----------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK  346 (385)
Q Consensus       284 ~~~-----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  346 (385)
                      -..           ....+..-|...-+....       .....  +.....+.+.|...|+.++|.++++.+.++
T Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          263 LPAILPYTASKLNPDIETVEAFGFPMPSDPLP-------EDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             HHHHGGGTC--------------CCCCC-CCC-------SSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cccccccccccccccchhHHHHHHHHHhcccc-------cccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            000           111122222111100000       00012  667777888899999999999999988654

>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=98.05  E-value=0.00011  Score=52.50  Aligned_cols=97  Identities=16%  Similarity=-0.001  Sum_probs=68.5

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ..|..+...+..   .|++++|...++...+.. +.+...+..+...+.+.|++++|...+++..+.+            
T Consensus         5 ~~~~~~~~~~~~---~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~------------   68 (118)
T 1elw_A            5 NELKEKGNKALS---VGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK------------   68 (118)
T ss_dssp             HHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHH---cccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC------------
Confidence            344555555444   788888888888887753 3356677777778888888888888887765433            


Q ss_pred             HHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                             +.+...+..+..++...|++++|...+++..+.
T Consensus        69 -------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           69 -------PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             -------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             -------cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence                   245667777777888888888888888877664

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.03  E-value=1.7e-05  Score=58.26  Aligned_cols=93  Identities=9%  Similarity=-0.017  Sum_probs=78.3

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc--h---hhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC----cchHHHHHHHH
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY--T---CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT----CVIWGALLGAC  359 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~---~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~----~~~~~~li~~~  359 (385)
                      .+...+...|++++|...|+.+.+..+  .   ..+..+..++.+.|++++|...|++.... |+    ...+..+..+|
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~   86 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQ   86 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHH
Confidence            345667788999999999999988766  3   57788899999999999999999988663 44    45678888999


Q ss_pred             HhcCChHHHHHHHHHHHhccccC
Q 040338          360 CSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       360 ~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ...|++++|...++++.+..|..
T Consensus        87 ~~~g~~~~A~~~~~~~~~~~p~~  109 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVATQYPGS  109 (129)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTS
T ss_pred             HHcCCHHHHHHHHHHHHHHCCCC
Confidence            99999999999999999887754

>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=98.02  E-value=1e-05  Score=59.35  Aligned_cols=94  Identities=7%  Similarity=-0.015  Sum_probs=77.1

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-C-------cchHHHHH
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-T-------CVIWGALL  356 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~-------~~~~~~li  356 (385)
                      +..+...+...|++++|...+++.....+  ...+..+...+...|++++|...+++.... | +       ..+|..+.
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la   86 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHH
Confidence            45666777788889999999998887766  777788888999999999999999887653 2 1       66788888


Q ss_pred             HHHHhcCChHHHHHHHHHHHhcccc
Q 040338          357 GACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ..|...|++++|...+++..+..+.
T Consensus        87 ~~~~~~~~~~~A~~~~~~~~~~~~~  111 (131)
T 1elr_A           87 NSYFKEEKYKDAIHFYNKSLAEHRT  111 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCC
Confidence            9999999999999999998887653

>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=98.02  E-value=9.9e-06  Score=59.80  Aligned_cols=100  Identities=11%  Similarity=-0.018  Sum_probs=80.8

Q ss_pred             hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHH
Q 040338           88 SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus        88 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      ..+..+...+.+.|++++|++.|++..+.+                   +.+...|+.+..+|.+.|++++|+..+++..
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-------------------p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al   69 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD-------------------PSNITFYNNKAAVYFEEKKFAECVQFCEKAV   69 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHH
Confidence            457778889999999999999998876554                   4567889999999999999999999999987


Q ss_pred             HCC--CCCC----HhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          168 NHG--FGLS----SMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       168 ~~g--~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      +..  ..++    ..+|..+-.++...|++++|++.|+..+....
T Consensus        70 ~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~~~  114 (127)
T 4gcn_A           70 EVGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLSEFR  114 (127)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSC
T ss_pred             HhCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc
Confidence            642  1122    23567777888899999999999999887643

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.02  E-value=2.6e-05  Score=65.46  Aligned_cols=129  Identities=12%  Similarity=-0.111  Sum_probs=90.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC--Ccch
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER--DLVS  142 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~  142 (385)
                      .|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...+..                   .|  ....
T Consensus       115 ~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-------------------d~~~~~~a  173 (282)
T 4f3v_A          115 QGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-------------------DKFLAGAA  173 (282)
T ss_dssp             HTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-------------------CHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-------------------CcccHHHH
Confidence            688888888887776643  333255555567777788888888886442211                   11  1236


Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC--HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGFGLS--SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      +..+-.++.+.|++++|+..|++.......|.  .........++.+.|+.++|...|+++....+.  ...+..|
T Consensus       174 ~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~--~~~~~aL  247 (282)
T 4f3v_A          174 GVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE--PKVAAAL  247 (282)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC--HHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc--HHHHHHH
Confidence            77788899999999999999999875433254  234556667788999999999999999998754  4444333

>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=98.01  E-value=1.6e-05  Score=59.15  Aligned_cols=95  Identities=5%  Similarity=-0.203  Sum_probs=76.4

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhc
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSH  362 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~  362 (385)
                      .+..+...+...|++++|...|+......+  ...+..+..++...|++++|...+++.... | +...|..+..+|...
T Consensus        11 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~   90 (137)
T 3q49_B           11 ELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEM   90 (137)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHH
Confidence            345556666777888888888888877776  777888888899999999999998887652 4 466788888899999


Q ss_pred             CChHHHHHHHHHHHhcccc
Q 040338          363 YNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       363 g~~~~a~~~~~~~~~~~~~  381 (385)
                      |++++|...+++..+..|.
T Consensus        91 ~~~~~A~~~~~~a~~~~p~  109 (137)
T 3q49_B           91 ESYDEAIANLQRAYSLAKE  109 (137)
T ss_dssp             TCHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHChh
Confidence            9999999999998887765

>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=98.01  E-value=1.3e-05  Score=64.20  Aligned_cols=64  Identities=8%  Similarity=-0.163  Sum_probs=34.5

Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ..+..+..+|.+.|++++|+..++.....  .+...|..+..+|...|++++|...+++..+..|.
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~  154 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPN  154 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC
Confidence            34445555555556666665555555431  23445555555555566666666666555555443

>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=98.01  E-value=2.8e-05  Score=68.02  Aligned_cols=151  Identities=11%  Similarity=-0.001  Sum_probs=113.1

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC-----
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD-----  139 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~-----  139 (385)
                      .+++++|...++...+.. +-+...+..+...|.+.|++++|...|++..+...                   .+     
T Consensus       126 L~~~~~A~~~~~~a~~~~-p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p-------------------~~~~~~~  185 (336)
T 1p5q_A          126 LKSFEKAKESWEMNSEEK-LEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLE-------------------YESSFSN  185 (336)
T ss_dssp             EEEEECCCCGGGCCHHHH-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-------------------TCCCCCS
T ss_pred             EeecccccchhcCCHHHH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhh-------------------ccccCCh
Confidence            345566666665544432 22567888899999999999999999988765432                   22     


Q ss_pred             ----------cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCc
Q 040338          140 ----------LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLD  209 (385)
Q Consensus       140 ----------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  209 (385)
                                ..+|..+..+|.+.|++++|+..|++..+.. +.+...|..+..++...|++++|...|+..++..+. +
T Consensus       186 ~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~  263 (336)
T 1p5q_A          186 EEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-N  263 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-C
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC-C
Confidence                      4789999999999999999999999998862 336788889999999999999999999999987542 2


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHH-HHHHHhcc
Q 040338          210 VFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKA-DLAFELMS  259 (385)
Q Consensus       210 ~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A-~~~~~~m~  259 (385)
                                            ..++..+...+.+.|+.++| ..+|..|.
T Consensus       264 ----------------------~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          264 ----------------------KAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             ----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                  23445566666666777777 44555554

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.00  E-value=4.9e-05  Score=57.91  Aligned_cols=135  Identities=13%  Similarity=-0.056  Sum_probs=90.7

Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAM  311 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  311 (385)
                      ..++..+...+...|++++|+..+++..+...           ..++  ......++..+...+...|++++|...+++.
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-----------~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a   75 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAK-----------EFGD--KAAERIAYSNLGNAYIFLGEFETASEYYKKT   75 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----------HHTC--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHH-----------HhCC--chHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34667888888999999999999988764100           0000  0000013344444455555556666655554


Q ss_pred             Hhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----C----CcchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          312 AKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----P----TCVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       312 ~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p----~~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      .....        ...+..+...+...|++++|.+.+++....    .    ...++..+...|...|++++|.+.+++.
T Consensus        76 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  155 (164)
T 3ro3_A           76 LLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  155 (164)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            44322        556777888899999999999998877541    1    1346778889999999999999999998


Q ss_pred             Hhcc
Q 040338          376 LQLD  379 (385)
Q Consensus       376 ~~~~  379 (385)
                      .+..
T Consensus       156 ~~~~  159 (164)
T 3ro3_A          156 LEIS  159 (164)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7653

>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=98.00  E-value=5.3e-05  Score=64.40  Aligned_cols=98  Identities=8%  Similarity=-0.158  Sum_probs=81.2

Q ss_pred             hhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHH
Q 040338           49 LFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRL  128 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a  128 (385)
                      ...+..+-..+..   .|++++|...++...+.. +.+...|..+..+|.+.|++++|...+++..+.+           
T Consensus         4 a~~~~~~g~~~~~---~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-----------   68 (281)
T 2c2l_A            4 AQELKEQGNRLFV---GRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-----------   68 (281)
T ss_dssp             HHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-----------
T ss_pred             HHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-----------
Confidence            3455555566555   899999999999999874 3377888999999999999999999999987765           


Q ss_pred             HHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          129 LIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       129 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                              +.+...+..+..++...|++++|...|++..+.
T Consensus        69 --------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  101 (281)
T 2c2l_A           69 --------GQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL  101 (281)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             --------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                    456778899999999999999999999988764

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.00  E-value=2.3e-05  Score=59.82  Aligned_cols=92  Identities=9%  Similarity=-0.110  Sum_probs=69.6

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CC----cc
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PT----CV  350 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~----~~  350 (385)
                      ++..+...+...|++++|...+++..+...        ...+..+...+...|++++|.+.+++....    ++    ..
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            455666666777777777777777665433        357778888899999999999999876542    12    44


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhc
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                      .+..+...+...|++++|...+++..+.
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~  118 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAI  118 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            6778888899999999999999988754

>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=97.98  E-value=0.0001  Score=54.65  Aligned_cols=101  Identities=8%  Similarity=-0.161  Sum_probs=80.4

Q ss_pred             CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccch
Q 040338           46 PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGI  125 (385)
Q Consensus        46 ~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~  125 (385)
                      ..+...|..+-..+..   .|++++|...|+...+.. +.+...|..+..+|...|++++|...|++..+.+        
T Consensus         6 ~~~~~~~~~~g~~~~~---~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--------   73 (137)
T 3q49_B            6 SPSAQELKEQGNRLFV---GRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD--------   73 (137)
T ss_dssp             CCCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------
T ss_pred             cccHHHHHHHHHHHHH---hCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--------
Confidence            3455666667777656   899999999999988874 3367788888899999999999999998876544        


Q ss_pred             HHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          126 IRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       126 ~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                                 +.+...|..+..++...|++++|...|++..+.
T Consensus        74 -----------p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           74 -----------GQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             -----------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -----------chhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence                       356778888889999999999999999888764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.98  E-value=4.8e-05  Score=58.72  Aligned_cols=100  Identities=10%  Similarity=-0.055  Sum_probs=81.5

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +...+..+...+.+.|++++|+..|++..+.+                   +.+...|..+..+|.+.|++++|+..|++
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~   70 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-------------------PANPIYLSNRAAAYSASGQHEKAAEDAEL   70 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CcCHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            45667778888888999999999988876554                   35677888888999999999999999999


Q ss_pred             HHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          166 LWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       166 m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      ..+.  .| +...|..+..++...|++++|...|+..++...
T Consensus        71 al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  110 (164)
T 3sz7_A           71 ATVV--DPKYSKAWSRLGLARFDMADYKGAKEAYEKGIEAEG  110 (164)
T ss_dssp             HHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHS
T ss_pred             HHHh--CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            8875  34 577788888888999999999999998888654

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.97  E-value=7.9e-06  Score=59.26  Aligned_cols=86  Identities=6%  Similarity=-0.018  Sum_probs=70.3

Q ss_pred             ccCChhhHHHHHHHHHhcc---c--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFT---Y--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~---~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      ..|++++|+..|++..+.+   +  ...+..+...|.+.|++++|++.|++..+. | +...+..+..+|...|++++|.
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            3578889999999999883   4  788888999999999999999999988763 4 4667888999999999999999


Q ss_pred             HHHHHHHhccccC
Q 040338          370 LVMRNLLQLDVKV  382 (385)
Q Consensus       370 ~~~~~~~~~~~~~  382 (385)
                      ..+++.++..|.+
T Consensus        82 ~~~~~al~~~p~~   94 (117)
T 3k9i_A           82 ELLLKIIAETSDD   94 (117)
T ss_dssp             HHHHHHHHHHCCC
T ss_pred             HHHHHHHHhCCCc
Confidence            9999998887665

>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=97.96  E-value=5.3e-05  Score=55.41  Aligned_cols=112  Identities=5%  Similarity=0.009  Sum_probs=85.5

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      ..|..+...+..   .|++++|...++...+.. +.+...+..+...|...|++++|...+++..+.+.           
T Consensus         5 ~~~~~l~~~~~~---~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-----------   69 (131)
T 1elr_A            5 LKEKELGNDAYK---KKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR-----------   69 (131)
T ss_dssp             HHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH-----------
T ss_pred             HHHHHHHHHHHH---hcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc-----------
Confidence            345666666555   899999999999999875 44678889999999999999999999988754332           


Q ss_pred             HHhcCCCCCC----cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040338          130 IMFQKMPERD----LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS  183 (385)
Q Consensus       130 ~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  183 (385)
                          .. .++    ..+|..+...+...|++++|...|++..+.  .|+......+..
T Consensus        70 ----~~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~  120 (131)
T 1elr_A           70 ----EN-REDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQ  120 (131)
T ss_dssp             ----HS-TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHH
T ss_pred             ----cc-chhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHH
Confidence                00 122    567888889999999999999999999885  456555444443

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.91  E-value=2.4e-05  Score=68.55  Aligned_cols=144  Identities=7%  Similarity=-0.074  Sum_probs=83.0

Q ss_pred             hHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHH---HHHHHHHHhcccCChhhHHHH
Q 040338          233 QIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFF---FFVSLLSGCSHSGPVTKGKHY  307 (385)
Q Consensus       233 ~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~---~~~~l~~~~~~~~~~~~a~~~  307 (385)
                      ..+..+...+.+.|++++|+..|++..+  |+...       +...|+.+++...+   +|..+..+|.+.|++++|...
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~-------~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~  252 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFM-------FQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGH  252 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHH-------HTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchh-------hhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4456777888899999999999998765  32221       11222223333333   788888999999999999999


Q ss_pred             HHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-cchHHHHHHH-HHhcCChHHHHHHHHHHHhccccC
Q 040338          308 FTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-CVIWGALLGA-CCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       308 ~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-~~~~~~li~~-~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +++..+..+  ...+..+..+|...|++++|.+.|++..+. |+ ...+..+... ....+..+++...|++|.+..|.+
T Consensus       253 ~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~~p~~  332 (338)
T 2if4_A          253 CNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMYKGIFKGKDEG  332 (338)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC----------------------------------------
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCC
Confidence            999988877  788888999999999999999999999874 53 4455555554 334567788999999999888765


Q ss_pred             C
Q 040338          383 F  383 (385)
Q Consensus       383 ~  383 (385)
                      +
T Consensus       333 ~  333 (338)
T 2if4_A          333 G  333 (338)
T ss_dssp             -
T ss_pred             C
Confidence            4

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.90  E-value=9.8e-05  Score=61.99  Aligned_cols=172  Identities=15%  Similarity=0.015  Sum_probs=108.7

Q ss_pred             CccCccchhhHHHHHHHhCCCCchHHHHHH-----------HHHHHhcCCCC-------CCc------------------
Q 040338          187 SVYDLEWGPHLHSRVVHMEPSLDVFVGSGL-----------IDMYLKCGCNG-------IES------------------  230 (385)
Q Consensus       187 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-----------i~~~~~~g~~~-------~~~------------------  230 (385)
                      ..++...|.+.|.++....+. ....|..+           ...+.....+.       ..|                  
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~-~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDES-ACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             cCCCHHHHHHHHHHHHHhChh-hhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            578889999999999887642 33344433           22222222111       111                  


Q ss_pred             ----hhhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhH
Q 040338          231 ----SIQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKG  304 (385)
Q Consensus       231 ----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a  304 (385)
                          -...+-.....+...|++++|.++|+.+..  |+......+.                      ..+.+.+++++|
T Consensus        97 ~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~~~~~~a----------------------~l~~~~~r~~dA  154 (282)
T 4f3v_A           97 PVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAGSEHLVAWMKA----------------------VVYGAAERWTDV  154 (282)
T ss_dssp             ECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTTCHHHHHHHHH----------------------HHHHHTTCHHHH
T ss_pred             ccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCchHHHHHHH----------------------HHHHHcCCHHHH
Confidence                123334456667777788888888777764  2111222222                      244556667777


Q ss_pred             HHHHHHHHhccc----hhhHHHHHHHHHccCCHHHHHHHHHhCCCCC---C--cchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          305 KHYFTAMAKFTY----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKP---T--CVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       305 ~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p---~--~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      +..|+.......    ...+..+..++.+.|++++|++.|++....|   .  .........++.+.|+.++|..+|+++
T Consensus       155 ~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a  234 (282)
T 4f3v_A          155 IDQVKSAGKWPDKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWL  234 (282)
T ss_dssp             HHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHhhccCCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            777765544332    2356678888999999999999999886433   2  235566777888999999999999999


Q ss_pred             Hhcccc
Q 040338          376 LQLDVK  381 (385)
Q Consensus       376 ~~~~~~  381 (385)
                      ...+|.
T Consensus       235 ~a~~P~  240 (282)
T 4f3v_A          235 QTTHPE  240 (282)
T ss_dssp             HHHSCC
T ss_pred             HhcCCc
Confidence            888775

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.90  E-value=5e-05  Score=58.48  Aligned_cols=96  Identities=11%  Similarity=-0.067  Sum_probs=75.3

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhc------------------cc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKF------------------TY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-  346 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~------------------~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  346 (385)
                      +......+.+.|++++|...|.+....                  .+  ...+..+..+|.+.|++++|+..++..... 
T Consensus        14 ~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~   93 (162)
T 3rkv_A           14 LRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE   93 (162)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            444455556666666666666666554                  33  677888899999999999999999888762 


Q ss_pred             C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          347 P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       347 p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      | +...|..+..+|...|++++|...+++.++.+|.+.
T Consensus        94 p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~  131 (162)
T 3rkv_A           94 ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAA  131 (162)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGH
T ss_pred             CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCH
Confidence            4 567899999999999999999999999999888753

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.86  E-value=9.4e-06  Score=58.87  Aligned_cols=86  Identities=8%  Similarity=-0.134  Sum_probs=61.1

Q ss_pred             cCChHHHHHHHHHHHHhc--cCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcch
Q 040338           65 VGNIKMALHLHGLVKKFY--FVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVS  142 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~  142 (385)
                      .|++++|+..|++..+.+  -+.+...+..+..+|.+.|++++|+..|++..+.+                   +.+..+
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~~   63 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-------------------PNHQAL   63 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCchHH
Confidence            577888888888887754  23345677778888888888888888887776544                   345667


Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      +..+..++.+.|++++|+..|++..+.
T Consensus        64 ~~~l~~~~~~~g~~~~A~~~~~~al~~   90 (117)
T 3k9i_A           64 RVFYAMVLYNLGRYEQGVELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            777888888888888888888877664

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.85  E-value=0.00035  Score=52.27  Aligned_cols=98  Identities=12%  Similarity=0.027  Sum_probs=66.0

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC----chHHHhHHHHHHhcCChhHHHHHHHhccCCCcccccc
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD----ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKF  123 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~  123 (385)
                      +...+..+...+..   .|++++|...|+...+.  .|+    ...+..+..+|...|++++|...+++..+.+      
T Consensus        27 ~~~~~~~~a~~~~~---~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~------   95 (148)
T 2dba_A           27 SVEQLRKEGNELFK---CGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD------   95 (148)
T ss_dssp             CHHHHHHHHHHHHT---TTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT------
T ss_pred             HHHHHHHHHHHHHH---hCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC------
Confidence            34445555555444   78888888888877764  344    5667777777777788888877776654433      


Q ss_pred             chHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          124 GIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       124 ~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                                   +.+...|..+..++...|++++|...|++..+.
T Consensus        96 -------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           96 -------------GGDVKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             -------------SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             -------------ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence                         245566777777777777788887777777664

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.85  E-value=0.0002  Score=53.64  Aligned_cols=100  Identities=14%  Similarity=-0.005  Sum_probs=85.5

Q ss_pred             CCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC----cchHHHHHHHHHhCCCchHHH
Q 040338           85 SDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD----LVSWNTMISILTRHGFGFETL  160 (385)
Q Consensus        85 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~  160 (385)
                      .+...+..+...+.+.|++++|.+.|++..+.+                    |+    ...|..+..+|...|++++|+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--------------------~~~~~~~~~~~~~a~~~~~~~~~~~A~   85 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLD--------------------ATPQDQAVLHRNRAACHLKLEDYDKAE   85 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--------------------CCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--------------------ccchHHHHHHHHHHHHHHHHccHHHHH
Confidence            356778888899999999999999999887654                    33    677888899999999999999


Q ss_pred             HHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          161 CTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       161 ~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      ..+++..+.  .| +...+..+..++...|++++|...++...+..+
T Consensus        86 ~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p  130 (148)
T 2dba_A           86 TEASKAIEK--DGGDVKALYRRSQALEKLGRLDQAVLDLQRCVSLEP  130 (148)
T ss_dssp             HHHHHHHHH--TSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHhh--CccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC
Confidence            999998875  34 567788888899999999999999999998753

>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=97.85  E-value=0.00014  Score=57.98  Aligned_cols=147  Identities=9%  Similarity=-0.059  Sum_probs=98.4

Q ss_pred             hhhhHHHHHhhhCCC---ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCc----------------hHHHhH
Q 040338           33 LIDDDYRVFCDIGPR---YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDE----------------SIAKSS   93 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~----------------~~~~~l   93 (385)
                      +++.|...|+.-...   ....+..+-..+..   .|++++|...|++..+.... +.                .+|..+
T Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~---~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l   94 (198)
T 2fbn_A           19 FQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFK---KNEINEAIVKYKEALDFFIH-TEEWDDQILLDKKKNIEISCNLNL   94 (198)
T ss_dssp             ---CCCSGGGCCHHHHHHHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHTTTT-CTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hccccCchhhCCHHHHHHHHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHHHhc-ccccchhhHHHHHHHHHHHHHHHH
Confidence            667777776632211   23344444455444   89999999999999885322 22                678888


Q ss_pred             HHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC
Q 040338           94 IDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL  173 (385)
Q Consensus        94 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  173 (385)
                      ..+|.+.|++++|+..+++..+.+                   +.+...|..+..+|...|++++|...|++..+.  .|
T Consensus        95 a~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p  153 (198)
T 2fbn_A           95 ATCYNKNKDYPKAIDHASKVLKID-------------------KNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NP  153 (198)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-------------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--ST
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHhC-------------------cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CC
Confidence            899999999999999998876544                   456778888999999999999999999998875  44


Q ss_pred             -CHhhHHHHHHHhcCccCccchh-hHHHHHHHh
Q 040338          174 -SSMLYATAFSARASVYDLEWGP-HLHSRVVHM  204 (385)
Q Consensus       174 -~~~t~~~ll~~~~~~~~~~~a~-~~~~~~~~~  204 (385)
                       +...+..+..++...++..++. ..+..+...
T Consensus       154 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~  186 (198)
T 2fbn_A          154 NNLDIRNSYELCVNKLKEARKKDKLTFGGMFDK  186 (198)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHC------------
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence             5566677777777777766665 455555443

>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=97.81  E-value=0.00011  Score=62.43  Aligned_cols=95  Identities=5%  Similarity=-0.195  Sum_probs=79.7

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHY  363 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g  363 (385)
                      +..+...+...|++++|...+++..+..+  ...+..+..+|.+.|++++|.+.+++..+. | +...+..+..+|...|
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g   86 (281)
T 2c2l_A            7 LKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEME   86 (281)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC
Confidence            44556677788889999999999888777  778888899999999999999999988774 4 5667888899999999


Q ss_pred             ChHHHHHHHHHHHhccccC
Q 040338          364 NTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~  382 (385)
                      ++++|...+++..+.+|..
T Consensus        87 ~~~~A~~~~~~al~l~p~~  105 (281)
T 2c2l_A           87 SYDEAIANLQRAYSLAKEQ  105 (281)
T ss_dssp             CHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhCccc
Confidence            9999999999998887754

>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=97.78  E-value=8.5e-05  Score=68.31  Aligned_cols=114  Identities=7%  Similarity=-0.076  Sum_probs=89.8

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           64 CVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      ..|++++|.+.+++..+.. +.+..+|..+..+|.+.|++++|++.+++..+.+                   +.+..+|
T Consensus        18 ~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-------------------p~~~~~~   77 (477)
T 1wao_1           18 KAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-------------------KKYIKGY   77 (477)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-------------------TTCHHHH
T ss_pred             HhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-------------------CCCHHHH
Confidence            3799999999999999874 3367889999999999999999999998887655                   4567789


Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHH--hcCccCccchhhHHH
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSA--RASVYDLEWGPHLHS  199 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~--~~~~~~~~~a~~~~~  199 (385)
                      ..+..+|.+.|++++|++.|++..+.  .| +...+..+..+  +.+.|++++|++.++
T Consensus        78 ~~lg~~~~~~g~~~eA~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           78 YRRAASNMALGKFRAALRDYETVVKV--KPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH--STTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999999999999999999875  34 33444445444  788899999999988

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.77  E-value=0.00013  Score=53.13  Aligned_cols=95  Identities=11%  Similarity=-0.105  Sum_probs=76.7

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHH
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIM  131 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~  131 (385)
                      +..+-..+..   .|++++|...++...+.. +.+...|..+..++.+.|++++|+..|++..+.+              
T Consensus        20 ~~~~g~~~~~---~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--------------   81 (121)
T 1hxi_A           20 PMEEGLSMLK---LANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--------------   81 (121)
T ss_dssp             HHHHHHHHHH---TTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------------
T ss_pred             HHHHHHHHHH---cCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--------------
Confidence            3334444444   899999999999999874 3477888889999999999999999998876655              


Q ss_pred             hcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          132 FQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       132 ~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                           +.+...+..+..++.+.|++++|+..|++..+.
T Consensus        82 -----P~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           82 -----PKDIAVHAALAVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             -----TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             -----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                 356778888999999999999999999998763

>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=97.70  E-value=0.0042  Score=53.58  Aligned_cols=255  Identities=7%  Similarity=-0.066  Sum_probs=149.5

Q ss_pred             hhhHHHHHHHHHhhhccCChH-HHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC----------hhHHHHHHHhccCCC
Q 040338           49 LFTYNTMINGGVRCLCVGNIK-MALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA----------VDYAESAFLRMLNPS  117 (385)
Q Consensus        49 ~~~~~~li~~~~~~~~~~~~~-~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~  117 (385)
                      ...|..+...+......|.+. +|+++++.+...+.. +..+|+.--..+...+.          +++++.+++.+...+
T Consensus        26 i~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~nP~-~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~  104 (331)
T 3dss_A           26 LKLYQSATQAVFQKRQAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN  104 (331)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC
Confidence            455666666555444466655 899999999976422 34455554444433332          567777777776555


Q ss_pred             ccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCC--chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccC-ccch
Q 040338          118 LFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGF--GFETLCTFIELWNHGFGLSSMLYATAFSARASVYD-LEWG  194 (385)
Q Consensus       118 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~-~~~a  194 (385)
                                         +.+..+|+.-...+.+.++  +++++.+++++.+.. +-|.+.|+.-...+...|. ++++
T Consensus       105 -------------------PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~ee  164 (331)
T 3dss_A          105 -------------------PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEE  164 (331)
T ss_dssp             -------------------TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHH
T ss_pred             -------------------CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHH
Confidence                               4677888887777777774  789999999999863 2367777665555666676 4889


Q ss_pred             hhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHH
Q 040338          195 PHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLIS  271 (385)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~  271 (385)
                      ++.+..+++..+ -+...|+-....+.+.+.....++        ..-...+.++++++.++....  | |..+|+-+--
T Consensus       165 l~~~~~~I~~~p-~N~SAW~~R~~ll~~l~~~~~~~~--------~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~  235 (331)
T 3dss_A          165 LAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGP--------QGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRW  235 (331)
T ss_dssp             HHHHHHHHHHCS-CCHHHHHHHHHHHHHHSCCC--------------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHCC-CCHHHHHHHHHHHHHhhhcccccc--------ccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            999999998764 455566555444444321100000        000001346778888877764  4 5666665444


Q ss_pred             HHHhc-CCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccchhhHH--H---HHHHHHccCCHHHHHHHHHhCCC
Q 040338          272 AFSQA-GVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYFV--C---MVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       272 ~~~~~-g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~---li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      .+.+. |..+-.            -...+.++++++.++++.+..+...+.  +   +.......|..+++...+.++.+
T Consensus       236 ll~~~~~~~~~~------------~~~~~~l~~el~~~~elle~~pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          236 LLGAGSGRCELS------------VEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHSSSCGGGCC------------HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             HHHhccCccccc------------hHHHHHHHHHHHHHHHHHhhCcccchHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            44333 211000            011234567777777777766611221  1   22222345667777777777764

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.67  E-value=8.8e-05  Score=68.00  Aligned_cols=123  Identities=6%  Similarity=-0.068  Sum_probs=83.5

Q ss_pred             HHHHcCCChhHHHHHHHhccc-------C---C-hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHH
Q 040338          240 TMYAEGGSTQKADLAFELMSR-------R---N-MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYF  308 (385)
Q Consensus       240 ~~~~~~g~~~~A~~~~~~m~~-------~---~-~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~  308 (385)
                      ..+...|++++|+.++++..+       +   + ..+++.|..+|...|++++|+.++               +++..++
T Consensus       317 ~~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~---------------~~aL~i~  381 (490)
T 3n71_A          317 DKARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYA---------------RRMVDGY  381 (490)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHH---------------HHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHH---------------HHHHHHH
Confidence            345678999999999877653       1   1 246666777777777777776653               4444444


Q ss_pred             HHHHhccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---------CCc-chHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          309 TAMAKFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---------PTC-VIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       309 ~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---------p~~-~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      ++..-...   ..+++.|...|..+|++++|+.++++..+-         |++ .+.+.+-.++...+.+++|..+++++
T Consensus       382 ~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~  461 (490)
T 3n71_A          382 MKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKM  461 (490)
T ss_dssp             HHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44333333   667777888888888888888888776541         322 24556667777888888888888887


Q ss_pred             Hh
Q 040338          376 LQ  377 (385)
Q Consensus       376 ~~  377 (385)
                      .+
T Consensus       462 ~~  463 (490)
T 3n71_A          462 RE  463 (490)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.66  E-value=0.00025  Score=51.85  Aligned_cols=96  Identities=13%  Similarity=-0.098  Sum_probs=76.4

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCc---chHHHHHHHHHhCCCchHHHHHHHHH
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDL---VSWNTMISILTRHGFGFETLCTFIEL  166 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~m  166 (385)
                      +..+...+.+.|++++|.+.|++..+.++                   .+.   ..+..+..++.+.|++++|...|++.
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~p-------------------~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~   65 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELYP-------------------NGVYTPNALYWLGESYYATRNFQLAEAQFRDL   65 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCS-------------------SSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHCC-------------------CCcccHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            34456777889999999999988765432                   223   47777888999999999999999999


Q ss_pred             HHCCCCCC----HhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          167 WNHGFGLS----SMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       167 ~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      .+..  |+    ...+..+..++...|++++|...++.+.+..+
T Consensus        66 ~~~~--p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p  107 (129)
T 2xev_A           66 VSRY--PTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQYP  107 (129)
T ss_dssp             HHHC--TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST
T ss_pred             HHHC--CCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC
Confidence            8753  43    55677788889999999999999999998753

>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=97.65  E-value=7.1e-05  Score=68.43  Aligned_cols=146  Identities=5%  Similarity=-0.173  Sum_probs=108.3

Q ss_pred             hhhhHHHHHhhhCC--C-ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCC--------------chHHHhHHH
Q 040338           33 LIDDDYRVFCDIGP--R-YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSD--------------ESIAKSSID   95 (385)
Q Consensus        33 ~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~--------------~~~~~~li~   95 (385)
                      ++++|...|+....  | ....|..+-..+..   .|++++|...|++..+......              ..+|..+..
T Consensus       249 ~~~~A~~~~~~~~~~~~~~a~~~~~~G~~~~~---~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~  325 (457)
T 1kt0_A          249 SFEKAKESWEMDTKEKLEQAAIVKEKGTVYFK---GGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAM  325 (457)
T ss_dssp             EEECCCCGGGSCHHHHHHHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccCcchhhcCHHHHHHHHHHHHHHHHHHHh---CCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHH
Confidence            56666666654331  1 23456666666555   8999999999999998643221              578899999


Q ss_pred             HHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-C
Q 040338           96 MHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-S  174 (385)
Q Consensus        96 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~  174 (385)
                      +|.+.|++++|+..|++..+.+                   +.+...|..+..+|...|++++|+..|++..+.  .| +
T Consensus       326 ~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~  384 (457)
T 1kt0_A          326 CYLKLREYTKAVECCDKALGLD-------------------SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQN  384 (457)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C---
T ss_pred             HHHHhcCHHHHHHHHHHHHhcC-------------------CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCC
Confidence            9999999999999998887655                   357788999999999999999999999999874  55 4


Q ss_pred             HhhHHHHHHHhcCccCccchh-hHHHHHH
Q 040338          175 SMLYATAFSARASVYDLEWGP-HLHSRVV  202 (385)
Q Consensus       175 ~~t~~~ll~~~~~~~~~~~a~-~~~~~~~  202 (385)
                      ...+..+..++.+.++.+++. ..+..|.
T Consensus       385 ~~a~~~l~~~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          385 KAARLQISMCQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567777888888888877665 3444443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.64  E-value=6.2e-05  Score=69.01  Aligned_cols=81  Identities=6%  Similarity=-0.093  Sum_probs=62.9

Q ss_pred             ccCChhhHHHHHHHHHhccc----------hhhHHHHHHHHHccCCHHHHHHHHHhCCC---------CCC-cchHHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFTY----------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS---------KPT-CVIWGALL  356 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~----------~~~~~~li~~~~~~g~~~~A~~~~~~m~~---------~p~-~~~~~~li  356 (385)
                      ..|++++|..++++..+...          ..+++.|...|...|++++|..++++...         .|+ ..+++.|.
T Consensus       321 ~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  400 (490)
T 3n71_A          321 SEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAG  400 (490)
T ss_dssp             TTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            44556666666655544221          77888999999999999999999988765         133 34799999


Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 040338          357 GACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      ..|...|++++|..++++.++
T Consensus       401 ~~~~~~G~~~eA~~~~~~Al~  421 (490)
T 3n71_A          401 LTNWHAGHIEVGHGMICKAYA  421 (490)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999999999865

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.59  E-value=0.0015  Score=60.10  Aligned_cols=281  Identities=9%  Similarity=-0.059  Sum_probs=148.2

Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC-hhHHHHHHHhccCC-CccccccchHHHHHHhcCCCCCCcchH
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA-VDYAESAFLRMLNP-SLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      |+++.+..+|+..+..  .|+...|...+....+.+. .+....+|+..... |.                 ...+...|
T Consensus        28 ~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~-----------------d~~s~~iW   88 (493)
T 2uy1_A           28 KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFEN-----------------YWDSYGLY   88 (493)
T ss_dssp             TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTT-----------------CTTCHHHH
T ss_pred             CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCC-----------------CcccHHHH
Confidence            7899999999999884  5799999999988888763 34455666554321 11                 12355666


Q ss_pred             HHHHHHHH----hCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC---c--------------cCccchhhHHHHHH
Q 040338          144 NTMISILT----RHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS---V--------------YDLEWGPHLHSRVV  202 (385)
Q Consensus       144 ~~li~~~~----~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~---~--------------~~~~~a~~~~~~~~  202 (385)
                      ...+..+.    ..++.+.+.++|++....  ++..  +..+...|..   .              +.+..|..+++.+.
T Consensus        89 ~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~--P~~~--~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~  164 (493)
T 2uy1_A           89 KEYIEEEGKIEDEQTRIEKIRNGYMRALQT--PMGS--LSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQ  164 (493)
T ss_dssp             HHHHHHTSSCSSHHHHHHHHHHHHHHHHTS--CCTT--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhchhhhHHHHHHHHHHHHHHhC--hhhh--HHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHH
Confidence            66665543    234566777777777752  2211  0111111110   0              11111222222211


Q ss_pred             HhCCCCchHHHHHHHHH--------------------HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-C
Q 040338          203 HMEPSLDVFVGSGLIDM--------------------YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-R  261 (385)
Q Consensus       203 ~~~~~~~~~~~~~li~~--------------------~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~  261 (385)
                      ..-...+...|...+..                    |-+.= ...+.+...|-..+.-+.+.|+.+.|..+|++... |
T Consensus       165 ~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al-~~~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~P  243 (493)
T 2uy1_A          165 PLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYIL-DSFYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEMS  243 (493)
T ss_dssp             HHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHH-HHTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHH-HcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC
Confidence            10000011112111111                    11100 00233456777777788889999999999986654 3


Q ss_pred             Chh-hHHHHHHHHHhcCCCCch---------------------HHH-HHHHHHHHHhcccCChhhHHHHHHHHHhccc--
Q 040338          262 NMI-SWMVLISAFSQAGVLEKP---------------------RFF-FFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--  316 (385)
Q Consensus       262 ~~~-~~~~li~~~~~~g~~~~a---------------------~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--  316 (385)
                      +.. .+.    .|....+.++.                     ... ..|...+....+.++.+.|..+|++. +...  
T Consensus       244 ~~~~l~~----~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~~~~  318 (493)
T 2uy1_A          244 DGMFLSL----YYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNEGVG  318 (493)
T ss_dssp             CSSHHHH----HHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTSCCC
T ss_pred             CcHHHHH----HHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCCCCC
Confidence            221 111    12211111110                     000 04555555555677889999999988 3222  


Q ss_pred             hhhHHHHHHHHHccC-CHHHHHHHHHhCCCC-CC-cchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          317 TCYFVCMVDLLGLSG-LLGEAKKLIDEMPSK-PT-CVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       317 ~~~~~~li~~~~~~g-~~~~A~~~~~~m~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                      ...|......-...+ +.+.|..+|+..... |+ ...|...++...+.|+.+.|..+|+.+
T Consensus       319 ~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~~~aR~l~er~  380 (493)
T 2uy1_A          319 PHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENARALFKRL  380 (493)
T ss_dssp             HHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            233332222222233 688999999877653 33 334566677777888999998888875

>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=97.56  E-value=0.0003  Score=64.65  Aligned_cols=117  Identities=11%  Similarity=-0.073  Sum_probs=85.3

Q ss_pred             cccCCChHHHHHHHHHHHHcccchhhHHhhhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhcc
Q 040338            4 CGSLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYF   83 (385)
Q Consensus         4 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~   83 (385)
                      +.+.|++++|...++++++.                     .+.+...|..+-..+..   .|++++|.+.+++..+.. 
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~---------------------~p~~~~~~~~lg~~~~~---~g~~~~A~~~~~~al~l~-   70 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIEL---------------------NPSNAIYYGNRSLAYLR---TECYGYALGDATRAIELD-   70 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHH---------------------CTTCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHSC-
T ss_pred             HHHhCCHHHHHHHHHHHHHh---------------------CCccHHHHHHHHHHHHH---hcCHHHHHHHHHHHHHhC-
Confidence            34556666666666666552                     24457788888888777   899999999999999874 


Q ss_pred             CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHH--HHhCCCchHHHH
Q 040338           84 VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISI--LTRHGFGFETLC  161 (385)
Q Consensus        84 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~--~~~~~~~~~a~~  161 (385)
                      +.+...|..+..+|.+.|++++|.+.|++..+.+                   +.+...+..+..+  +.+.|++++|++
T Consensus        71 p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-------------------p~~~~~~~~l~~~~~~~~~g~~~~A~~  131 (477)
T 1wao_1           71 KKYIKGYYRRAASNMALGKFRAALRDYETVVKVK-------------------PHDKDAKMKYQECNKIVKQKAFERAIA  131 (477)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-------------------TTCTTHHHHHHHHHHHHHHHHHCCC--
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3467889999999999999999999998876544                   2344566666555  888899999999


Q ss_pred             HHH
Q 040338          162 TFI  164 (385)
Q Consensus       162 ~~~  164 (385)
                      .++
T Consensus       132 ~~~  134 (477)
T 1wao_1          132 GDE  134 (477)
T ss_dssp             ---
T ss_pred             ccc
Confidence            988

>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=97.54  E-value=0.00041  Score=63.38  Aligned_cols=138  Identities=12%  Similarity=0.001  Sum_probs=85.8

Q ss_pred             hhHHHHHHHHHHcCCChhHHHHHHHhccc--CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHH
Q 040338          232 IQIGKALVTMYAEGGSTQKADLAFELMSR--RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFT  309 (385)
Q Consensus       232 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~  309 (385)
                      ...+..+...+.+.|++++|+..|++..+  |+...+..   -...   -.......+|..+..+|.+.|++++|+..++
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~---~~~~---~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~  341 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSE---KESK---ASESFLLAAFLNLAMCYLKLREYTKAVECCD  341 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCH---HHHH---HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCCh---HHHH---HHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            34567788889999999999999998865  32100000   0000   0000001156666667777777777777777


Q ss_pred             HHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHH-HHHHH
Q 040338          310 AMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAEL-VMRNL  375 (385)
Q Consensus       310 ~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~-~~~~~  375 (385)
                      +..+..+  ...+..+..+|...|++++|+..|++..+. | +...+..+..++.+.++.+++.+ +++.|
T Consensus       342 ~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          342 KALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERDRRIYANM  412 (457)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777666  666777777777788888888877777653 3 44567777777777777765543 34444

>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=97.53  E-value=0.00038  Score=52.82  Aligned_cols=97  Identities=11%  Similarity=-0.014  Sum_probs=77.4

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccch--------------hhHHHHHHHHHccCCHHHHHHHHHhCCC--------
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTYT--------------CYFVCMVDLLGLSGLLGEAKKLIDEMPS--------  345 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--------------~~~~~li~~~~~~g~~~~A~~~~~~m~~--------  345 (385)
                      +......+...|++++|...|++..+..+.              ..|..+..++.+.|++++|+..+++..+        
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~   93 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL   93 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccC
Confidence            344555666778888888888887776652              2788889999999999999998887653        


Q ss_pred             CC-CcchH----HHHHHHHHhcCChHHHHHHHHHHHhccccCCC
Q 040338          346 KP-TCVIW----GALLGACCSHYNTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       346 ~p-~~~~~----~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  384 (385)
                      .| +...|    .....++...|++++|+..|++.++..|...+
T Consensus        94 ~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~  137 (159)
T 2hr2_A           94 NQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKG  137 (159)
T ss_dssp             TSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCS
T ss_pred             CCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHH
Confidence            34 44578    89999999999999999999999998887653

>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=97.51  E-value=0.00046  Score=61.07  Aligned_cols=95  Identities=6%  Similarity=-0.146  Sum_probs=66.7

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHh----------------ccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAK----------------FTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-  347 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~----------------~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-  347 (385)
                      +..+...+.+.|++++|...|++..+                ...  ...+..+..+|.+.|++++|++.+++..+. | 
T Consensus       226 ~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~  305 (370)
T 1ihg_A          226 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPS  305 (370)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCch
Confidence            33444444455555555555555444                222  667777888888888888888888887763 4 


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          348 TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       348 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +...|..+..+|...|++++|...+++..+..|.+
T Consensus       306 ~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~  340 (370)
T 1ihg_A          306 NTKALYRRAQGWQGLKEYDQALADLKKAQEIAPED  340 (370)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             hHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCC
Confidence            45678888888888888888888888888877654

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.50  E-value=0.00094  Score=51.15  Aligned_cols=100  Identities=10%  Similarity=-0.126  Sum_probs=72.2

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHhc-----------------cCCCchHHHhHHHHHHhcCChhHHHHHHHhcc
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKFY-----------------FVSDESIAKSSIDMHVKCGAVDYAESAFLRML  114 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g-----------------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  114 (385)
                      +...-..+..   .|++++|...|....+.-                 -+.+..+|..+..+|.+.|++++|+..+++..
T Consensus        14 ~~~~G~~~~~---~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           14 LRQKGNELFV---QKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH---cCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            4444444444   799999999999988750                 12234677778888888888888888887766


Q ss_pred             CCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH
Q 040338          115 NPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus       115 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  175 (385)
                      +.+                   +.+...|..+..+|...|++++|...|++..+.  .|+.
T Consensus        91 ~~~-------------------p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~  130 (162)
T 3rkv_A           91 KRE-------------------ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAA  130 (162)
T ss_dssp             HHS-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGG
T ss_pred             hcC-------------------CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCC
Confidence            544                   356677888888888888888888888887764  5543

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.48  E-value=0.00014  Score=51.52  Aligned_cols=94  Identities=12%  Similarity=-0.014  Sum_probs=66.1

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +...+..+...+.+.|++++|.+.|++..+.+                   +.+...|..+..++.+.|++++|+..+++
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~   63 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-------------------PQNPVGYSNKAMALIKLGEYTQAIQMCQQ   63 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-------------------CCCHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            45567777778888888888888887765544                   34567778888888888888888888888


Q ss_pred             HHHCCCCCC-------HhhHHHHHHHhcCccCccchhhHHHH
Q 040338          166 LWNHGFGLS-------SMLYATAFSARASVYDLEWGPHLHSR  200 (385)
Q Consensus       166 m~~~g~~p~-------~~t~~~ll~~~~~~~~~~~a~~~~~~  200 (385)
                      ..+.  .|+       ...+..+..++...|+.+.+...++.
T Consensus        64 al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  103 (111)
T 2l6j_A           64 GLRY--TSTAEHVAIRSKLQYRLELAQGAVGSVQIPVVEVDE  103 (111)
T ss_dssp             HHTS--CSSTTSHHHHHHHHHHHHHHHHHHHCCCCCSSSSSS
T ss_pred             HHHh--CCCccHHHHHHHHHHHHHHHHHHHHhHhhhHhHHHH
Confidence            8764  444       44555566666666777666655443

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=97.43  E-value=2.5e-05  Score=69.37  Aligned_cols=233  Identities=11%  Similarity=0.048  Sum_probs=171.2

Q ss_pred             hHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHH
Q 040338          125 IIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVH  203 (385)
Q Consensus       125 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~  203 (385)
                      +++|.++-+++..|  .+|..|..+..+.++..+|++-|       ++. |...|..++.+..+.|.+++-.+.+....+
T Consensus        41 ldRa~eyA~~~n~p--~VWs~LgkAqL~~~~v~eAIdsy-------IkA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk  111 (624)
T 3lvg_A           41 LDRAYEFAERCNEP--AVWSQLAKAQLQKGMVKEAIDSY-------IKADDPSSYMEVVQAANTSGNWEELVKYLQMARK  111 (624)
T ss_dssp             STTTTTSSSSCCCC--CCSSSHHHHTTTSSSCTTTTTSS-------CCCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTST
T ss_pred             cHHHHHHHHHhCCc--cHHHHHHHHHHccCchHHHHHHH-------HhCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            33444444444344  35778888888888888887666       332 566788888888889988888888777665


Q ss_pred             hCCCCchHHHHHHHHHHHhcCCCC------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----------------
Q 040338          204 MEPSLDVFVGSGLIDMYLKCGCNG------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----------------  260 (385)
Q Consensus       204 ~~~~~~~~~~~~li~~~~~~g~~~------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----------------  260 (385)
                      ..  -++.+=+.|+-+|++.++..      ..|++.-...+.+-|...|.++.|.-+|..+..                 
T Consensus       112 ~~--ke~~IDteLi~ayAk~~rL~elEefl~~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~A  189 (624)
T 3lvg_A          112 KA--RESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAA  189 (624)
T ss_dssp             TC--CSTTTTHHHHHHHHTSCSSSTTTSTTSCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSS
T ss_pred             Hh--cccccHHHHHHHHHhhCcHHHHHHHHcCCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            53  34445567888899888777      567777778889999999999999999887752                 


Q ss_pred             -------CChhhHHHHHHHHHhcCCCCchHHHH--------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHH
Q 040338          261 -------RNMISWMVLISAFSQAGVLEKPRFFF--------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCM  323 (385)
Q Consensus       261 -------~~~~~~~~li~~~~~~g~~~~a~~~~--------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~l  323 (385)
                             .++.||-.+-.+|...+.+.-|...-        -...++..|-..|-+++.+.+++.-.....  ..+|+-|
T Consensus       190 VdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvhadeL~elv~~YE~~G~f~ELIsLlEaglglErAHmGmFTEL  269 (624)
T 3lvg_A          190 VDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTEL  269 (624)
T ss_dssp             TTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCCSSCCSGGGSSSSTTCCCTTSTTTHHHHTTSTTCCHHHHHHH
T ss_pred             HHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhcccHHHHHHHHHHHHhCCCHHHHHHHHHHHhCCCchhHHHHHHH
Confidence                   37789999999999999988776443        455778888999999999999998774444  7888888


Q ss_pred             HHHHHccCCHHHHHHHHHhCCCC----------CCcchHHHHHHHHHhcCChHHHH
Q 040338          324 VDLLGLSGLLGEAKKLIDEMPSK----------PTCVIWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       324 i~~~~~~g~~~~A~~~~~~m~~~----------p~~~~~~~li~~~~~~g~~~~a~  369 (385)
                      .-.|++- +++...+-++-.-.+          -....|.-++-.|..-.+++.|.
T Consensus       270 aILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~  324 (624)
T 3lvg_A          270 AILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAI  324 (624)
T ss_dssp             HHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHH
Confidence            8888876 456666666555443          23456777777777777776554

>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=97.43  E-value=0.00099  Score=58.94  Aligned_cols=119  Identities=10%  Similarity=-0.057  Sum_probs=86.0

Q ss_pred             HHHHHHHHHhhhccCChHHHHHHHHHHHHh---------------ccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCC
Q 040338           52 YNTMINGGVRCLCVGNIKMALHLHGLVKKF---------------YFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNP  116 (385)
Q Consensus        52 ~~~li~~~~~~~~~~~~~~a~~~~~~m~~~---------------g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  116 (385)
                      |..+-..+.+   .|++++|++.+++..+.               --+.+..+|..+..+|.+.|++++|+..+++..+.
T Consensus       226 ~~~~g~~~~~---~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  302 (370)
T 1ihg_A          226 LKNIGNTFFK---SQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI  302 (370)
T ss_dssp             HHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHH---hcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh
Confidence            4445555444   89999999999998872               11234567888888888899999999998887765


Q ss_pred             CccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccch
Q 040338          117 SLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWG  194 (385)
Q Consensus       117 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a  194 (385)
                      +                   +.+...|..+..+|...|++++|+..|++..+.  .| +...+..+..++...++.+++
T Consensus       303 ~-------------------p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          303 D-------------------PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             C-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-------------------chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            5                   356778888888899999999999999888774  44 455555555555555554443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.35  E-value=0.00025  Score=50.85  Aligned_cols=78  Identities=12%  Similarity=-0.058  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhc
Q 040338          303 KGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQL  378 (385)
Q Consensus       303 ~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  378 (385)
                      .+...+++..+..+  ...+..+...|...|++++|++.|++.... | +...|..+..+|...|++++|...+++..+.
T Consensus         3 ~a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   82 (115)
T 2kat_A            3 AITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLAA   82 (115)
T ss_dssp             CHHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            45566666666555  556666666777777777777777666542 3 3446666677777777777777777776655


Q ss_pred             cc
Q 040338          379 DV  380 (385)
Q Consensus       379 ~~  380 (385)
                      .+
T Consensus        83 ~~   84 (115)
T 2kat_A           83 AQ   84 (115)
T ss_dssp             HH
T ss_pred             cc
Confidence            44

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.30  E-value=0.00057  Score=59.68  Aligned_cols=97  Identities=6%  Similarity=-0.209  Sum_probs=73.3

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--h-----------------hhHHHHHHHHHccCCHHHHHHHHHhCCCC-
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T-----------------CYFVCMVDLLGLSGLLGEAKKLIDEMPSK-  346 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~-----------------~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  346 (385)
                      .+..+...+.+.|++++|...|++......  .                 ..+..+..+|.+.|++++|+..+++.... 
T Consensus       181 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  260 (338)
T 2if4_A          181 RRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTEE  260 (338)
T ss_dssp             HHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            455556666667777777777777665444  1                 37888999999999999999999988663 


Q ss_pred             C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          347 P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       347 p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      | +...|..+..+|...|++++|...|++.++..|.+.
T Consensus       261 p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~  298 (338)
T 2if4_A          261 EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDK  298 (338)
T ss_dssp             TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCH
Confidence            4 677899999999999999999999999998887654

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.28  E-value=0.0001  Score=52.31  Aligned_cols=88  Identities=9%  Similarity=-0.082  Sum_probs=67.8

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC-------cchHHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT-------CVIWGALL  356 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-------~~~~~~li  356 (385)
                      .+..+...+...|++++|...+++..+..+  ...+..+..++.+.|++++|++.+++.... |+       ...+..+.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~   85 (111)
T 2l6j_A            6 KQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSKLQYRLE   85 (111)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHH
Confidence            355667778888999999999999888777  778888999999999999999999988764 55       44566666


Q ss_pred             HHHHhcCChHHHHHHHHH
Q 040338          357 GACCSHYNTKLAELVMRN  374 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~  374 (385)
                      .++...|+.+.|...+++
T Consensus        86 ~~~~~~~~~~~a~~~~~~  103 (111)
T 2l6j_A           86 LAQGAVGSVQIPVVEVDE  103 (111)
T ss_dssp             HHHHHHHCCCCCSSSSSS
T ss_pred             HHHHHHHhHhhhHhHHHH
Confidence            677777766666554443

>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=97.20  E-value=0.001  Score=49.56  Aligned_cols=91  Identities=11%  Similarity=-0.126  Sum_probs=76.5

Q ss_pred             HHHhcccCChhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCCCCcchHHHHHHHHHh----cC
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSKPTCVIWGALLGACCS----HY  363 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~----~g  363 (385)
                      ...|...+.+++|.+.|++..+.+.+.....|...|..    .+++++|.+.|++..+..+...+..|...|..    .+
T Consensus        32 g~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~  111 (138)
T 1klx_A           32 SLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLNDQDGCLILGYKQYAGKGVVK  111 (138)
T ss_dssp             HHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCC
T ss_pred             HHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCCCc
Confidence            34445556677799999999998888888888888888    89999999999998877788888899999998    89


Q ss_pred             ChHHHHHHHHHHHhccccC
Q 040338          364 NTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       364 ~~~~a~~~~~~~~~~~~~~  382 (385)
                      +.++|..++++..+.|..+
T Consensus       112 d~~~A~~~~~~Aa~~g~~~  130 (138)
T 1klx_A          112 NEKQAVKTFEKACRLGSED  130 (138)
T ss_dssp             CHHHHHHHHHHHHHTTCHH
T ss_pred             CHHHHHHHHHHHHHCCCHH
Confidence            9999999999998887643

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.16  E-value=0.00098  Score=47.65  Aligned_cols=79  Identities=9%  Similarity=-0.086  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHH
Q 040338           70 MALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISI  149 (385)
Q Consensus        70 ~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~  149 (385)
                      .++..++...+.. +.+...+..+...|...|++++|...|++..+.+                   +.+...|..+..+
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~~la~~   62 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-------------------PTYSVAWKWLGKT   62 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-------------------CCcHHHHHHHHHH
Confidence            3555666665543 2355667777777777777777777776665433                   2445567777777


Q ss_pred             HHhCCCchHHHHHHHHHHH
Q 040338          150 LTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       150 ~~~~~~~~~a~~~~~~m~~  168 (385)
                      +...|++++|...|++..+
T Consensus        63 ~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           63 LQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            7777777777777777654

>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=97.16  E-value=0.0036  Score=47.47  Aligned_cols=89  Identities=15%  Similarity=0.096  Sum_probs=70.2

Q ss_pred             cCChHHHHHHHHHHHHhccCC------Cc-----hHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhc
Q 040338           65 VGNIKMALHLHGLVKKFYFVS------DE-----SIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQ  133 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~------~~-----~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~  133 (385)
                      .|++++|+..|++..+.....      +.     ..|..+..++.+.|++++|+..+++..+               +|+
T Consensus        24 ~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~---------------l~n   88 (159)
T 2hr2_A           24 AGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH---------------YFN   88 (159)
T ss_dssp             HTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHH
T ss_pred             CCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---------------hhh
Confidence            799999999999999864321      22     3899999999999999999999876543               332


Q ss_pred             CCC---CCCcchH----HHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          134 KMP---ERDLVSW----NTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       134 ~~~---~~~~~~~----~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      +-.   +.+...|    ...-.++...|++++|+..|++..+
T Consensus        89 ~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           89 RRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            221   3455677    8888999999999999999999865

>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=97.04  E-value=0.055  Score=46.58  Aligned_cols=215  Identities=11%  Similarity=-0.035  Sum_probs=128.4

Q ss_pred             chHHHHHHH---HHhCCCch-HHHHHHHHHHHCCCCCCH-hhHHHHHHHhcCccC----------ccchhhHHHHHHHhC
Q 040338          141 VSWNTMISI---LTRHGFGF-ETLCTFIELWNHGFGLSS-MLYATAFSARASVYD----------LEWGPHLHSRVVHME  205 (385)
Q Consensus       141 ~~~~~li~~---~~~~~~~~-~a~~~~~~m~~~g~~p~~-~t~~~ll~~~~~~~~----------~~~a~~~~~~~~~~~  205 (385)
                      ..|..+...   ..+.|.++ +|+++++.+...  .|+. ..++.--..+...+.          +++++.+++.+....
T Consensus        27 ~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~--nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~  104 (331)
T 3dss_A           27 KLYQSATQAVFQKRQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN  104 (331)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC
Confidence            345444433   34556655 799999999874  5543 334432222222222          567788888887765


Q ss_pred             CCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCC--ChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCC-
Q 040338          206 PSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGG--STQKADLAFELMSRR---NMISWMVLISAFSQAGVL-  279 (385)
Q Consensus       206 ~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g--~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~-  279 (385)
                      + -+..+|                      +.-.-.+.+.|  ++++++.+++.+.+.   |-.+|+.-.-.+...|.. 
T Consensus       105 P-Kny~aW----------------------~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~  161 (331)
T 3dss_A          105 P-KSYGTW----------------------HHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAP  161 (331)
T ss_dssp             T-TCHHHH----------------------HHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCH
T ss_pred             C-CCHHHH----------------------HHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCH
Confidence            4 233333                      33333344444  467888888887763   445555555555666663 


Q ss_pred             CchHHHH------------HHHHHHHHhccc--------------CChhhHHHHHHHHHhccc--hhhHHHHHHHHHcc-
Q 040338          280 EKPRFFF------------FFVSLLSGCSHS--------------GPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLS-  330 (385)
Q Consensus       280 ~~a~~~~------------~~~~l~~~~~~~--------------~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~-  330 (385)
                      +++++.+            +|+.........              +.++++.+.+.......+  ...|+-+--.+.+. 
T Consensus       162 ~eel~~~~~~I~~~p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~  241 (331)
T 3dss_A          162 AEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGS  241 (331)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSS
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcc
Confidence            5666665            444333333322              457888899998888777  55555333334443 


Q ss_pred             ----------CCHHHHHHHHHhCCC-CCCcchHHHHHH-----HHHhcCChHHHHHHHHHHHhcccc
Q 040338          331 ----------GLLGEAKKLIDEMPS-KPTCVIWGALLG-----ACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       331 ----------g~~~~A~~~~~~m~~-~p~~~~~~~li~-----~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                                +.++++++.++++.+ .|+. .|..+..     +....|..+++...++++++.+|.
T Consensus       242 ~~~~~~~~~~~~l~~el~~~~elle~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~Dp~  307 (331)
T 3dss_A          242 GRCELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPM  307 (331)
T ss_dssp             CGGGCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHCGG
T ss_pred             CccccchHHHHHHHHHHHHHHHHHhhCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCcc
Confidence                      457888888888876 3665 4443222     233467788999999999988875

>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=97.03  E-value=0.011  Score=55.33  Aligned_cols=201  Identities=6%  Similarity=-0.118  Sum_probs=135.3

Q ss_pred             hHHHHHHHHHhhhcc-CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC----------hhHHHHHHHhccCCCcc
Q 040338           51 TYNTMINGGVRCLCV-GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA----------VDYAESAFLRMLNPSLF  119 (385)
Q Consensus        51 ~~~~li~~~~~~~~~-~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~~~  119 (385)
                      .|..+...+...... ..-++|++.++++.+.+.. +..+|+.--.++...|+          ++++++.++++.+.+  
T Consensus        27 ~y~~~~~~~~~~~~~~~~~eeal~~~~~~l~~nP~-~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~--  103 (567)
T 1dce_A           27 LYQSATQAVFQKRQAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN--  103 (567)
T ss_dssp             HHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC--
Confidence            344444433332223 4556889999999987532 55677777777777666          889999998887666  


Q ss_pred             ccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCC--CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCcc-Cccchhh
Q 040338          120 CWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHG--FGFETLCTFIELWNHGFGLSSMLYATAFSARASVY-DLEWGPH  196 (385)
Q Consensus       120 ~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~-~~~~a~~  196 (385)
                                       +.+..+|+.--..+.+.+  +++++++.++++.+.. +-|.+.|+.--..+.+.| .++++.+
T Consensus       104 -----------------pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~  165 (567)
T 1dce_A          104 -----------------PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELA  165 (567)
T ss_dssp             -----------------TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHH
T ss_pred             -----------------CCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHH
Confidence                             467788988888888899  6699999999999863 237777877666666777 7788888


Q ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHH
Q 040338          197 LHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAF  273 (385)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~  273 (385)
                      .++.+++..+ -+...|+-....+.+.+......+..        -...+.++++++.++...+  | |...|+-+-..+
T Consensus       166 ~~~~~I~~~p-~n~saW~~r~~ll~~l~~~~~~~~~~--------~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll  236 (567)
T 1dce_A          166 FTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQG--------RLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLL  236 (567)
T ss_dssp             HHHTTTTTTC-CCHHHHHHHHHHHHHHSCCCCSSSCC--------SSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHCC-CCccHHHHHHHHHHhhcccccccccc--------cccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHH
Confidence            8888877654 35555655544444432110000000        0001356888888877764  4 678888888888


Q ss_pred             HhcCCCCc
Q 040338          274 SQAGVLEK  281 (385)
Q Consensus       274 ~~~g~~~~  281 (385)
                      .+.++.++
T Consensus       237 ~~~~~~~~  244 (567)
T 1dce_A          237 GRAEPHDV  244 (567)
T ss_dssp             SCCCCCSC
T ss_pred             hcCCCccc
Confidence            88887655

>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=97.02  E-value=0.00066  Score=51.40  Aligned_cols=98  Identities=8%  Similarity=-0.155  Sum_probs=77.1

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCCh----------hHHHHHHHhccCCCccccccchHHHHHHhcC
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAV----------DYAESAFLRMLNPSLFCWKFGIIRLLIMFQK  134 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~----------~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~  134 (385)
                      .+.+++|.+.++...+.. +.+...|+.+-.++.+.+++          ++|+..|++..+.+                 
T Consensus        15 ~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld-----------------   76 (158)
T 1zu2_A           15 ILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-----------------   76 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-----------------
T ss_pred             HhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC-----------------
Confidence            578899999999999875 44788888888888888765          47888877776555                 


Q ss_pred             CCCCCcchHHHHHHHHHhCC-----------CchHHHHHHHHHHHCCCCCCHhhHHHHHHH
Q 040338          135 MPERDLVSWNTMISILTRHG-----------FGFETLCTFIELWNHGFGLSSMLYATAFSA  184 (385)
Q Consensus       135 ~~~~~~~~~~~li~~~~~~~-----------~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  184 (385)
                        +.+..+|..+-.+|...|           ++++|+..|++..+  +.|+...|...+..
T Consensus        77 --P~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~  133 (158)
T 1zu2_A           77 --PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEM  133 (158)
T ss_dssp             --TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHH
T ss_pred             --cCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHH
Confidence              356778999999998764           89999999999988  47877777665553

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.99  E-value=0.0013  Score=45.70  Aligned_cols=64  Identities=11%  Similarity=0.074  Sum_probs=34.5

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      +...+..+..+|.+.|++++|+..|++..+.+                   +.+...|..+..+|...|++++|...|++
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            34455555555555566666665555554433                   23344555555555566666666655555


Q ss_pred             HHH
Q 040338          166 LWN  168 (385)
Q Consensus       166 m~~  168 (385)
                      ..+
T Consensus        67 al~   69 (100)
T 3ma5_A           67 GIE   69 (100)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            543

>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=96.93  E-value=0.0066  Score=45.06  Aligned_cols=113  Identities=3%  Similarity=-0.216  Sum_probs=78.6

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .+++++|.+.|++..+.| .|+  ..  |-..|...+.+++|.+.|++..+.                     .+...+.
T Consensus         8 ~~d~~~A~~~~~~aa~~g-~~~--a~--lg~~y~~g~~~~~A~~~~~~Aa~~---------------------g~~~a~~   61 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN-EMF--GC--LSLVSNSQINKQKLFQYLSKACEL---------------------NSGNGCR   61 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CTT--HH--HHHHTCTTSCHHHHHHHHHHHHHT---------------------TCHHHHH
T ss_pred             ccCHHHHHHHHHHHHcCC-CHh--hh--HHHHHHcCCCHHHHHHHHHHHHcC---------------------CCHHHHH
Confidence            467788888888888776 222  22  666666667777788888776543                     3445666


Q ss_pred             HHHHHHHh----CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC----ccCccchhhHHHHHHHhCC
Q 040338          145 TMISILTR----HGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS----VYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       145 ~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~  206 (385)
                      .|-..|..    .+++++|+.+|++..+.|   +...+..|-..|..    .++.++|.+.++...+.|.
T Consensus        62 ~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           62 FLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCCCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            77777776    778888888888887764   34455555555555    6788888888888887764

>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=96.92  E-value=0.0015  Score=58.81  Aligned_cols=81  Identities=9%  Similarity=-0.049  Sum_probs=65.1

Q ss_pred             ccCChhhHHHHHHHHHhccc----------hhhHHHHHHHHHccCCHHHHHHHHHhCCC---------CCC-cchHHHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFTY----------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS---------KPT-CVIWGALL  356 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~----------~~~~~~li~~~~~~g~~~~A~~~~~~m~~---------~p~-~~~~~~li  356 (385)
                      ..|++++|..++++..+...          ..+++.+..+|...|++++|+.++++...         .|+ ..+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            45678888888887665322          67788899999999999999999988765         133 34799999


Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 040338          357 GACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      ..|...|++++|..++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            999999999999999998865

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.91  E-value=0.0032  Score=42.36  Aligned_cols=29  Identities=10%  Similarity=0.126  Sum_probs=14.5

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      ..++..+...+.+.|++++|...|++..+
T Consensus        43 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           43 AEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            34444444555555555555555555444

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.84  E-value=0.0056  Score=41.08  Aligned_cols=82  Identities=10%  Similarity=0.029  Sum_probs=63.8

Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHH
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLID  218 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  218 (385)
                      +...+..+...+...|++++|+..|++..+.. +.+...+..+..++...|++++|...+++..+..+ .+...+..+-.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCHHHHHHHHH
Confidence            35678888899999999999999999998752 23567788889999999999999999999998753 23445544444


Q ss_pred             HHHh
Q 040338          219 MYLK  222 (385)
Q Consensus       219 ~~~~  222 (385)
                      .+.+
T Consensus        86 ~~~~   89 (91)
T 1na3_A           86 AKQK   89 (91)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            4433

>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=96.76  E-value=0.00081  Score=50.92  Aligned_cols=87  Identities=13%  Similarity=-0.091  Sum_probs=71.4

Q ss_pred             ccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCH----------HHHHHHHHhCCC-CC-CcchHHHHHHHHHhc
Q 040338          297 HSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLL----------GEAKKLIDEMPS-KP-TCVIWGALLGACCSH  362 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~----------~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~  362 (385)
                      +.+.+++|.+.++...+..+  ...+..+..++...+++          ++|+..|++..+ .| +...|..+..+|.+.
T Consensus        14 r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~l   93 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSF   93 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHh
Confidence            34567889999999988888  78888888888887765          589999988876 35 456899999999887


Q ss_pred             C-----------ChHHHHHHHHHHHhccccCC
Q 040338          363 Y-----------NTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       363 g-----------~~~~a~~~~~~~~~~~~~~~  383 (385)
                      |           ++++|++.|++.++.+|..+
T Consensus        94 g~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~  125 (158)
T 1zu2_A           94 AFLTPDETEAKHNFDLATQFFQQAVDEQPDNT  125 (158)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             cccCcchhhhhccHHHHHHHHHHHHHhCCCCH
Confidence            5           89999999999999988753

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.74  E-value=0.016  Score=40.09  Aligned_cols=57  Identities=7%  Similarity=-0.032  Sum_probs=36.4

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      +..+...+...|++++|...|++..+..+  ...+..+..+|...|++++|.+.|++..
T Consensus        10 ~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A           10 RYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34445555556666666666776666655  5566667777777777777777666543

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.69  E-value=0.0012  Score=45.53  Aligned_cols=86  Identities=6%  Similarity=-0.079  Sum_probs=64.2

Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc--hh-hHHHHHHHHHccCCHHHHHHHHHhCCCC-CCcc-hHHHHHHHHHhcCCh
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY--TC-YFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTCV-IWGALLGACCSHYNT  365 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~--~~-~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~-~~~~li~~~~~~g~~  365 (385)
                      ....+...|++++|...+++..+..+  .. .+..+..+|...|++++|.+.|++.... |+.. .+..        +.+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~--------~~~   77 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSPALQAR--------KMV   77 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHH--------HHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHH--------HHH
Confidence            34556778899999999999888777  56 7888889999999999999999888663 4432 2211        566


Q ss_pred             HHHHHHHHHHHhccccCCC
Q 040338          366 KLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~~~  384 (385)
                      .++...+++....+|.++.
T Consensus        78 ~~a~~~~~~~~~~~p~~~~   96 (99)
T 2kc7_A           78 MDILNFYNKDMYNQLEHHH   96 (99)
T ss_dssp             HHHHHHHCCTTHHHHCCSS
T ss_pred             HHHHHHHHHHhccCccccc
Confidence            7777777777776666553

>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=96.69  E-value=0.004  Score=56.12  Aligned_cols=86  Identities=14%  Similarity=-0.087  Sum_probs=64.4

Q ss_pred             HHHhcccCChhhHHHHHHHHHhccc----------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC---------CC-cch
Q 040338          292 LSGCSHSGPVTKGKHYFTAMAKFTY----------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK---------PT-CVI  351 (385)
Q Consensus       292 ~~~~~~~~~~~~a~~~~~~~~~~~~----------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---------p~-~~~  351 (385)
                      +..+...|++++|..++++..+...          ..+++.+...|...|++++|+.++++...-         |+ ..+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            4445566788888888887765322          667788888888889999988888876541         33 346


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          352 WGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       352 ~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      ++.|...|...|++++|..++++..+
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            88888889999999999888888764

>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=96.66  E-value=0.027  Score=52.71  Aligned_cols=139  Identities=6%  Similarity=-0.111  Sum_probs=105.4

Q ss_pred             CChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCC----------CCchHHHH------------HHHHHHHHhcccC-
Q 040338          246 GSTQKADLAFELMSR--R-NMISWMVLISAFSQAGV----------LEKPRFFF------------FFVSLLSGCSHSG-  299 (385)
Q Consensus       246 g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~----------~~~a~~~~------------~~~~l~~~~~~~~-  299 (385)
                      ..-++|++.++++.+  | +...|+.--.++...|+          ++++++.+            +|..-...+.+.+ 
T Consensus        43 ~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           43 ELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSS
T ss_pred             CCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHccc
Confidence            345678888888876  3 34556554555555555          66677666            7777777777888 


Q ss_pred             -ChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC-CHHHHHHHHHhCCCC--CCcchHHHHHHHHHhc-----------
Q 040338          300 -PVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG-LLGEAKKLIDEMPSK--PTCVIWGALLGACCSH-----------  362 (385)
Q Consensus       300 -~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g-~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~-----------  362 (385)
                       +++++...++++.+..+  ...|+.-...+.+.| .++++.+.++++.+.  -|...|+.....+.+.           
T Consensus       123 ~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~~~~~  202 (567)
T 1dce_A          123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGR  202 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCS
T ss_pred             ccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccccccccc
Confidence             67999999999999888  667777777777788 899999999999875  4667788777776653           


Q ss_pred             ---CChHHHHHHHHHHHhccccCCC
Q 040338          363 ---YNTKLAELVMRNLLQLDVKVFG  384 (385)
Q Consensus       363 ---g~~~~a~~~~~~~~~~~~~~~~  384 (385)
                         +.++++++.+++.+..+|.+.+
T Consensus       203 ~~~~~~~eel~~~~~ai~~~P~~~s  227 (567)
T 1dce_A          203 LPENVLLKELELVQNAFFTDPNDQS  227 (567)
T ss_dssp             SCHHHHHHHHHHHHHHHHHCSSCSH
T ss_pred             ccHHHHHHHHHHHHHHHhhCCCCcc
Confidence               5679999999999998887653

>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=96.40  E-value=0.0046  Score=55.68  Aligned_cols=87  Identities=8%  Similarity=-0.114  Sum_probs=56.4

Q ss_pred             cCCChhHHHHHHHhccc-------C---C-hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHH
Q 040338          244 EGGSTQKADLAFELMSR-------R---N-MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMA  312 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~-------~---~-~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  312 (385)
                      ..|++++|+.++++..+       +   + ..+++.|..+|...|++++|+.++               +++..++++..
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~---------------~~aL~i~~~~l  374 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYG---------------QKIIKPYSKHY  374 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHH---------------HHHHHHHHHHS
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHH---------------HHHHHHHHHHc
Confidence            45677777777766543       1   1 145555555565555555555442               44444444433


Q ss_pred             hccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          313 KFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       313 ~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      -...   ..+++.|...|..+|++++|+.++++..+
T Consensus       375 G~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          375 PVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            3222   77888999999999999999999988764

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.36  E-value=0.17  Score=36.62  Aligned_cols=138  Identities=12%  Similarity=-0.105  Sum_probs=97.6

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|.+++..++..+...+   .+..-||-+|.-....-+-+...++++.+-+.--.+.-|++.....-+-.+. .+..-.+
T Consensus        20 dG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C~~~~n-~~se~vd   95 (172)
T 1wy6_A           20 DGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINN-TLNEHVN   95 (172)
T ss_dssp             TTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTT-CCCHHHH
T ss_pred             hhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHHHHHhc-chHHHHH
Confidence            57778888887777764   3556677776666666666666666666544322222244444444444432 3445677


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                      ..++.+...|+-+.-.+++..+.. ..+|+....-.+..+|.+.|+..++.+++.+.-+.|++
T Consensus        96 ~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           96 KALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            788999999999999999988643 35778888889999999999999999999999999874

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.32  E-value=0.012  Score=57.64  Aligned_cols=166  Identities=16%  Similarity=-0.018  Sum_probs=86.0

Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      ..++..+.+.|.+++|+++.+.       |. .    -+......|+++.|.++.+.+                      
T Consensus       633 ~~~~~~l~~~~~~~~a~~~~~~-------~~-~----~f~~~l~~~~~~~A~~~~~~~----------------------  678 (814)
T 3mkq_A          633 TKIARFLEGQEYYEEALNISPD-------QD-Q----KFELALKVGQLTLARDLLTDE----------------------  678 (814)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCCC-------HH-H----HHHHHHHHTCHHHHHHHHTTC----------------------
T ss_pred             HHHHHHHHhCCChHHheecCCC-------cc-h----heehhhhcCCHHHHHHHHHhh----------------------
Confidence            5666666777777777655521       11 1    122234456777666654332                      


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhh
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTK  303 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~  303 (385)
                            .+...|..+...+.+.|+++.|++.|..+.+     |..+...|...|+.+..      ..+.......|+.+.
T Consensus       679 ------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d-----~~~l~~l~~~~~~~~~~------~~~~~~a~~~~~~~~  741 (814)
T 3mkq_A          679 ------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD-----LESLFLLHSSFNNKEGL------VTLAKDAETTGKFNL  741 (814)
T ss_dssp             ------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC-----HHHHHHHHHHTTCHHHH------HHHHHHHHHTTCHHH
T ss_pred             ------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC-----hhhhHHHHHHcCCHHHH------HHHHHHHHHcCchHH
Confidence                  1233456666666666677777777776653     22333333333333221      122333334445555


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCc----chHHHHHHHHHhcCChHHH
Q 040338          304 GKHYFTAMAKFTYTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTC----VIWGALLGACCSHYNTKLA  368 (385)
Q Consensus       304 a~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~----~~~~~li~~~~~~g~~~~a  368 (385)
                      |...+-..      .-+...++.|.+.+++++|..+-+...  |..    .........+...|+.+.|
T Consensus       742 A~~~~~~~------g~~~~a~~~~~~~~~~~~A~~lA~~~~--~~~~~i~~~~~~~~~~L~~~~~~~~a  802 (814)
T 3mkq_A          742 AFNAYWIA------GDIQGAKDLLIKSQRFSEAAFLGSTYG--LGDNEVNDIVTKWKENLILNGKNTVS  802 (814)
T ss_dssp             HHHHHHHH------TCHHHHHHHHHHTTCHHHHHHHHHHTT--CCHHHHHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHHc------CCHHHHHHHHHHcCChHHHHHHHHHhC--CChHHHHHHHHHHHHHHHhccchhHH
Confidence            44444332      334445667777888888888877654  233    2333344455556654433

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.26  E-value=0.06  Score=46.79  Aligned_cols=145  Identities=8%  Similarity=-0.090  Sum_probs=97.9

Q ss_pred             CCCChhhHHHHHHHHHhhhc--cCChHHHHHHHHHHHHhccCCC-chHHHhHHHHHHh---cCChh-HHHHHHHhccCCC
Q 040338           45 GPRYLFTYNTMINGGVRCLC--VGNIKMALHLHGLVKKFYFVSD-ESIAKSSIDMHVK---CGAVD-YAESAFLRMLNPS  117 (385)
Q Consensus        45 ~~~~~~~~~~li~~~~~~~~--~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~---~g~~~-~a~~~~~~m~~~~  117 (385)
                      +..+...|...+++.....+  .....+|..+|++..+.  .|+ ...|..+..+|.-   .+.+. ....-        
T Consensus       190 ~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~--------  259 (372)
T 3ly7_A          190 LPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVDIVRHSQHPLDEKQLAA--------  259 (372)
T ss_dssp             SCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH--------
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhccCCCchhhHHH--------
Confidence            35578899999988765322  34568999999999986  454 3555554444431   11111 00000        


Q ss_pred             ccccccchHHHHHHhcC--CCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchh
Q 040338          118 LFCWKFGIIRLLIMFQK--MPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGP  195 (385)
Q Consensus       118 ~~~~~~~~~~a~~~~~~--~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  195 (385)
                             +..+.+-...  ..+.+..+|..+...+...|++++|...+++....+  |+...|..+-..+.-.|++++|.
T Consensus       260 -------l~~a~~a~~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~  330 (372)
T 3ly7_A          260 -------LNTEIDNIVTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAA  330 (372)
T ss_dssp             -------HHHHHHHHHTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             -------HHHHHHHHHhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHH
Confidence                   0111111111  114577788887777777899999999999999874  88888878888888999999999


Q ss_pred             hHHHHHHHhCCCC
Q 040338          196 HLHSRVVHMEPSL  208 (385)
Q Consensus       196 ~~~~~~~~~~~~~  208 (385)
                      +.+++....++.+
T Consensus       331 e~~~~AlrL~P~~  343 (372)
T 3ly7_A          331 DAYLTAFNLRPGA  343 (372)
T ss_dssp             HHHHHHHHHSCSH
T ss_pred             HHHHHHHhcCCCc
Confidence            9999999886543

>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=96.24  E-value=0.0078  Score=54.21  Aligned_cols=93  Identities=12%  Similarity=0.026  Sum_probs=58.7

Q ss_pred             HHHHHHcCCChhHHHHHHHhccc-------C-C---hhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHH
Q 040338          238 LVTMYAEGGSTQKADLAFELMSR-------R-N---MISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKH  306 (385)
Q Consensus       238 li~~~~~~g~~~~A~~~~~~m~~-------~-~---~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~  306 (385)
                      .+..+.+.|++++|+.++++..+       + +   ..+++.|..+|...|++++|+.++               +++..
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~---------------~~~L~  357 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYG---------------TRTME  357 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHH---------------HHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHH---------------HHHHH
Confidence            35556667788888887776643       1 1   134555555555555555554442               33344


Q ss_pred             HHHHHHhccc---hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          307 YFTAMAKFTY---TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       307 ~~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      +++...-...   ..+++.|...|...|++++|+.++++..+
T Consensus       358 i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          358 PYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            4443322222   77788899999999999999999988765

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.17  E-value=0.033  Score=54.56  Aligned_cols=71  Identities=8%  Similarity=-0.048  Sum_probs=39.4

Q ss_pred             cchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHH
Q 040338          123 FGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVV  202 (385)
Q Consensus       123 ~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  202 (385)
                      |+++.|+++.+.+  .+...|..|...+.+.++++.|.++|..+..         |..+...+...|+.+...++-+...
T Consensus       666 ~~~~~A~~~~~~~--~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~  734 (814)
T 3mkq_A          666 GQLTLARDLLTDE--SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAE  734 (814)
T ss_dssp             TCHHHHHHHHTTC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhh--CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHH
Confidence            3344444443333  3456788888888888888888888877643         2233333333455544444444443


Q ss_pred             Hh
Q 040338          203 HM  204 (385)
Q Consensus       203 ~~  204 (385)
                      ..
T Consensus       735 ~~  736 (814)
T 3mkq_A          735 TT  736 (814)
T ss_dssp             HT
T ss_pred             Hc
Confidence            33

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.15  E-value=0.074  Score=38.50  Aligned_cols=134  Identities=9%  Similarity=-0.059  Sum_probs=87.8

Q ss_pred             cCCChhHHHHHHHhcccC-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHh--cccCChhhHHHHHHHHHhccc-hhh
Q 040338          244 EGGSTQKADLAFELMSRR-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGC--SHSGPVTKGKHYFTAMAKFTY-TCY  319 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~-~~~  319 (385)
                      -.|.+++..++..+..++ +..-||-+|--....-+-+-..+++  ..+...+  ...|++......+-   ..+. ...
T Consensus        19 ldG~v~qGveii~k~~~ssni~E~NW~ICNiiD~a~C~y~v~vL--d~IGkiFDis~C~NlKrVi~C~~---~~n~~se~   93 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVL--DKIGSYFDLDKCQNLKSVVECGV---INNTLNEH   93 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHH--HHHGGGSCGGGCSCTHHHHHHHH---HTTCCCHH
T ss_pred             HhhhHHHHHHHHHHHcCCCCccccceeeeecchhhchhHHHHHH--HHHhhhcCcHhhhcHHHHHHHHH---HhcchHHH
Confidence            357888888888887763 4455555554433332222222111  1111111  22344443333332   3333 777


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhC-CCC-CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEM-PSK-PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m-~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ++.-++.+..+|+-+...+++.++ ... |++...-.+..||.+.|+..+|.+++++..+.|++.
T Consensus        94 vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~kE  158 (172)
T 1wy6_A           94 VNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEKE  158 (172)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhHH
Confidence            788899999999999999999995 443 788888889999999999999999999999998864

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.09  E-value=0.0065  Score=41.71  Aligned_cols=61  Identities=13%  Similarity=0.010  Sum_probs=52.5

Q ss_pred             HHHHHHccCCHHHHHHHHHhCCCC-C-Ccc-hHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          323 MVDLLGLSGLLGEAKKLIDEMPSK-P-TCV-IWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       323 li~~~~~~g~~~~A~~~~~~m~~~-p-~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ....+.+.|++++|.+.|++..+. | +.. .|..+..+|...|++++|...+++.++.+|...
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~   69 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSP   69 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTST
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcH
Confidence            456788899999999999988763 4 456 888899999999999999999999999888754

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.90  E-value=0.33  Score=37.22  Aligned_cols=125  Identities=16%  Similarity=0.074  Sum_probs=88.6

Q ss_pred             HHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH----HHHHHHHHhcccCChhhHHHHHHHHHhcc
Q 040338          240 TMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF----FFVSLLSGCSHSGPVTKGKHYFTAMAKFT  315 (385)
Q Consensus       240 ~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  315 (385)
                      ....+.|+++.|.++.+.+  .+...|..|.......|+++-|.+.|    -+..+.-.|.-.|+.++...+-+....  
T Consensus        13 ~LAL~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           13 DLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHSFDKLSFLYLVTGDVNKLSKMQNIAQT--   88 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTCHHHHHHHHHHHTCHHHHHHHHHHHHH--
T ss_pred             HHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHHH--
Confidence            4456789999999998877  46788999999999999999988877    455555555556666555544443333  


Q ss_pred             chhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHHHH
Q 040338          316 YTCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNL  375 (385)
Q Consensus       316 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  375 (385)
                       ..-++.-...+...|+++++.++|.+...-|      --+-.....|..+.|.++.+++
T Consensus        89 -~g~~n~af~~~l~lGdv~~~i~lL~~~~r~~------eA~~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           89 -REDFGSMLLNTFYNNSTKERSSIFAEGGSLP------LAYAVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             -TTCHHHHHHHHHHHTCHHHHHHHHHHTTCHH------HHHHHHHHTTCHHHHHHHHHHT
T ss_pred             -CccHHHHHHHHHHcCCHHHHHHHHHHCCChH------HHHHHHHHcCcHHHHHHHHHHh
Confidence             3455666667778999999999998876522      1222233467778888887776

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.42  E-value=0.008  Score=44.97  Aligned_cols=85  Identities=15%  Similarity=-0.067  Sum_probs=59.8

Q ss_pred             cCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccC---CHHHHHHHHHhCCCC--C--CcchHHHHHHHHHhcCChHHH
Q 040338          298 SGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSG---LLGEAKKLIDEMPSK--P--TCVIWGALLGACCSHYNTKLA  368 (385)
Q Consensus       298 ~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g---~~~~A~~~~~~m~~~--p--~~~~~~~li~~~~~~g~~~~a  368 (385)
                      ...+..+++-|.+..+.+.  ..+...+..++++++   ++++++.+|++..+.  |  +...+-.|.-+|.+.|++++|
T Consensus        11 ~~~l~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A   90 (152)
T 1pc2_A           11 VEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKA   90 (152)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHH
Confidence            3445666777777666555  556666777888877   566888888877653  3  233455566677888899999


Q ss_pred             HHHHHHHHhccccC
Q 040338          369 ELVMRNLLQLDVKV  382 (385)
Q Consensus       369 ~~~~~~~~~~~~~~  382 (385)
                      .+.++.+++..|.+
T Consensus        91 ~~y~~~lL~ieP~n  104 (152)
T 1pc2_A           91 LKYVRGLLQTEPQN  104 (152)
T ss_dssp             HHHHHHHHHHCTTC
T ss_pred             HHHHHHHHhcCCCC
Confidence            99998888888765

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.19  E-value=0.077  Score=36.06  Aligned_cols=66  Identities=8%  Similarity=-0.105  Sum_probs=37.4

Q ss_pred             CCchHHHhHHHHHHhcCC---hhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHH
Q 040338           85 SDESIAKSSIDMHVKCGA---VDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLC  161 (385)
Q Consensus        85 ~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  161 (385)
                      .++..+..+..++...++   .++|..++++..+.+                   +.++.+...+...+.+.|++++|+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-------------------p~~~rA~~~lg~~~~~~g~y~~Ai~   64 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-------------------PYNEAALSLIANDHFISFRFQEAID   64 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-------------------cCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            345555555555543332   466666666655444                   2445555555666666666666666


Q ss_pred             HHHHHHHC
Q 040338          162 TFIELWNH  169 (385)
Q Consensus       162 ~~~~m~~~  169 (385)
                      .|+++.+.
T Consensus        65 ~w~~~l~~   72 (93)
T 3bee_A           65 TWVLLLDS   72 (93)
T ss_dssp             HHHHHHTC
T ss_pred             HHHHHHhh
Confidence            66666654

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=95.15  E-value=0.37  Score=41.89  Aligned_cols=128  Identities=7%  Similarity=-0.063  Sum_probs=83.2

Q ss_pred             hhhhHHHHHhhhC--CCC-hhhHHHHHHHHHhhhccC--ChHHHHH---HHHHHHH-hccCCCchHHHhHHHHHHhcCCh
Q 040338           33 LIDDDYRVFCDIG--PRY-LFTYNTMINGGVRCLCVG--NIKMALH---LHGLVKK-FYFVSDESIAKSSIDMHVKCGAV  103 (385)
Q Consensus        33 ~~~~A~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~--~~~~a~~---~~~~m~~-~g~~~~~~~~~~li~~~~~~g~~  103 (385)
                      +..+|..+|++..  .|+ ...|..+--++......+  .......   .+..... ...+.+..+|..+...+...|++
T Consensus       214 ~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~~~~~~~a~~~~alal~~l~~gd~  293 (372)
T 3ly7_A          214 SLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELNNLSIIYQIKAVSALVKGKT  293 (372)
T ss_dssp             HHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTCGGGTTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHhCCCH
Confidence            6789999999877  454 234443333332111111  1111111   2221111 12356778888887777778999


Q ss_pred             hHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHH
Q 040338          104 DYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAF  182 (385)
Q Consensus       104 ~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll  182 (385)
                      ++|...+++....+                    |+...|..+-..+.-.|++++|.+.|++....  .|...||...=
T Consensus       294 d~A~~~l~rAl~Ln--------------------~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~~~~  350 (372)
T 3ly7_A          294 DESYQAINTGIDLE--------------------MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLYWIE  350 (372)
T ss_dssp             HHHHHHHHHHHHHC--------------------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--------------------CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHHHHh
Confidence            99999998876543                    66667777888889999999999999998874  77777765443

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.05  E-value=0.018  Score=51.50  Aligned_cols=168  Identities=8%  Similarity=-0.026  Sum_probs=102.7

Q ss_pred             CCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCc-----cc
Q 040338           46 PRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL-----FC  120 (385)
Q Consensus        46 ~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-----~~  120 (385)
                      ..|+..|..+|..   +.+.|.+++-.+.+.-..+..-  ++.+=+.|+-+|++.+++.+-.+++..-...++     .+
T Consensus        80 A~Dps~y~eVi~~---A~~~~~~edLv~yL~MaRk~~k--e~~IDteLi~ayAk~~rL~elEefl~~~N~A~iq~VGDrc  154 (624)
T 3lvg_A           80 ADDPSSYMEVVQA---ANTSGNWEELVKYLQMARKKAR--ESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRC  154 (624)
T ss_dssp             CSCCCSSSHHHHH---TTTSSCCTTHHHHHHTTSTTCC--STTTTHHHHHHHHTSCSSSTTTSTTSCCSSSCTHHHHHHH
T ss_pred             CCChHHHHHHHHH---HHhCCCHHHHHHHHHHHHHHhc--ccccHHHHHHHHHhhCcHHHHHHHHcCCCcccHHHHHHHH
Confidence            3466778889998   4458999999988877666533  444446999999999988776655433222111     01


Q ss_pred             cc-cchHHHHHHhcCCC------------------------CCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH
Q 040338          121 WK-FGIIRLLIMFQKMP------------------------ERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus       121 ~~-~~~~~a~~~~~~~~------------------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  175 (385)
                      +. |.++.|.-+|..++                        ..++.||.-+-.+|...+.+.-|.-.--.+.-   .|| 
T Consensus       155 f~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIv---had-  230 (624)
T 3lvg_A          155 YDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVV---HAD-  230 (624)
T ss_dssp             HHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHC---CSS-
T ss_pred             HHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhcc---cHH-
Confidence            11 33333333333332                        24778899999999988888776544333332   222 


Q ss_pred             hhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          176 MLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       176 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                       -...++..|-+.|.+++-+.+++.-+.. -......|+.|.-.|++-.
T Consensus       231 -eL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsKY~  277 (624)
T 3lvg_A          231 -ELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK  277 (624)
T ss_dssp             -CCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHSSC
T ss_pred             -HHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHhcC
Confidence             1224566677777777777777765521 2345566666666666543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.03  E-value=0.043  Score=41.01  Aligned_cols=86  Identities=8%  Similarity=-0.200  Sum_probs=55.0

Q ss_pred             ChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcC---ChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC--Ccc
Q 040338           67 NIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCG---AVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER--DLV  141 (385)
Q Consensus        67 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~--~~~  141 (385)
                      .+..+.+-|.+..+.|. ++..+...+..++++.+   ++++++.+|++..+.+                   .|  +..
T Consensus        13 ~l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-------------------~p~~~rd   72 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-------------------SKEEQRD   72 (152)
T ss_dssp             HHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-------------------CHHHHHH
T ss_pred             HHHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-------------------CccchHH
Confidence            34555566666655553 57777777777777776   5567777777665433                   12  233


Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHGFGLS  174 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  174 (385)
                      .+-.|--+|.+.|++++|.+.++.+.+.  .|+
T Consensus        73 ~lY~LAv~~~kl~~Y~~A~~y~~~lL~i--eP~  103 (152)
T 1pc2_A           73 YVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQ  103 (152)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhc--CCC
Confidence            4444555667888888888888888773  563

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=94.86  E-value=0.15  Score=42.55  Aligned_cols=82  Identities=10%  Similarity=0.074  Sum_probs=62.8

Q ss_pred             ChhhHHHHHHHHHhccc----hhhHHHHHHHHHcc-----CCHHHHHHHHHhCCC-CCC--cchHHHHHHHHHhc-CChH
Q 040338          300 PVTKGKHYFTAMAKFTY----TCYFVCMVDLLGLS-----GLLGEAKKLIDEMPS-KPT--CVIWGALLGACCSH-YNTK  366 (385)
Q Consensus       300 ~~~~a~~~~~~~~~~~~----~~~~~~li~~~~~~-----g~~~~A~~~~~~m~~-~p~--~~~~~~li~~~~~~-g~~~  366 (385)
                      ....|...+++..+..+    ...+..+...|.+.     |+.+.|.+.|++..+ .|+  ..++......++.. |+.+
T Consensus       178 ~l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~  257 (301)
T 3u64_A          178 TVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRA  257 (301)
T ss_dssp             HHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHH
T ss_pred             hHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHH
Confidence            35677777787777776    55777788888874     888888888888776 363  66777777877774 8888


Q ss_pred             HHHHHHHHHHhcccc
Q 040338          367 LAELVMRNLLQLDVK  381 (385)
Q Consensus       367 ~a~~~~~~~~~~~~~  381 (385)
                      ++.+.+++.++..+.
T Consensus       258 ~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          258 GFDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHcCCCC
Confidence            888888888888777

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.23  E-value=0.065  Score=37.28  Aligned_cols=55  Identities=9%  Similarity=-0.023  Sum_probs=30.5

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhcc-------c--hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFT-------Y--TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~-------~--~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                      .+...+...++++.|...++...+..       .  ..++..+..+|.+.|+++.|...+++..
T Consensus        10 ~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al   73 (104)
T 2v5f_A           10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLL   73 (104)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            34445555666666666666555431       1  4455555566666666666666655554

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.17  E-value=0.2  Score=34.72  Aligned_cols=68  Identities=9%  Similarity=-0.089  Sum_probs=55.6

Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHCC------CCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNHG------FGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      +..-+-.|...+.+.++++.|..+|+...+.-      -.+....+..+..++.+.|+++.|...+++..+..+
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P   77 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDP   77 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCC
Confidence            44556678889999999999999999987631      123466788899999999999999999999998754

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=93.85  E-value=0.35  Score=32.73  Aligned_cols=48  Identities=6%  Similarity=-0.120  Sum_probs=32.8

Q ss_pred             hhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CC
Q 040338          301 VTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PT  348 (385)
Q Consensus       301 ~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~  348 (385)
                      .++|..++++..+..+  +.....+...+.+.|++++|+..|+.+.+. |+
T Consensus        25 ~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A           25 TDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT
T ss_pred             CHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            5667777777776666  666666667777777777777777776654 44

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=93.80  E-value=0.76  Score=35.23  Aligned_cols=104  Identities=13%  Similarity=0.095  Sum_probs=65.3

Q ss_pred             HHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC
Q 040338           95 DMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLS  174 (385)
Q Consensus        95 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  174 (385)
                      ....+.|+++.|.++.+.+                        .+...|..|.......|+++-|.+.|.+..+      
T Consensus        13 ~LAL~lg~l~~A~e~a~~l------------------------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D------   62 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL------------------------NDSITWERLIQEALAQGNASLAEMIYQTQHS------   62 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH------------------------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC------
T ss_pred             HHHHhcCCHHHHHHHHHHh------------------------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC------
Confidence            4455678888888877654                        3456799999999999999999999888643      


Q ss_pred             HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHH
Q 040338          175 SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLA  254 (385)
Q Consensus       175 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  254 (385)
                         |..+.-.|.-.|+.+.-.++-+.....|-                            ++.-...+...|+++++.++
T Consensus        63 ---~~~L~~Ly~~tg~~e~L~kla~iA~~~g~----------------------------~n~af~~~l~lGdv~~~i~l  111 (177)
T 3mkq_B           63 ---FDKLSFLYLVTGDVNKLSKMQNIAQTRED----------------------------FGSMLLNTFYNNSTKERSSI  111 (177)
T ss_dssp             ---HHHHHHHHHHHTCHHHHHHHHHHHHHTTC----------------------------HHHHHHHHHHHTCHHHHHHH
T ss_pred             ---HHHHHHHHHHhCCHHHHHHHHHHHHHCcc----------------------------HHHHHHHHHHcCCHHHHHHH
Confidence               23333344445665554444444443332                            13333445556777777777


Q ss_pred             HHhcc
Q 040338          255 FELMS  259 (385)
Q Consensus       255 ~~~m~  259 (385)
                      |.+..
T Consensus       112 L~~~~  116 (177)
T 3mkq_B          112 FAEGG  116 (177)
T ss_dssp             HHHTT
T ss_pred             HHHCC
Confidence            65543

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=93.10  E-value=0.36  Score=34.64  Aligned_cols=84  Identities=14%  Similarity=-0.061  Sum_probs=59.6

Q ss_pred             CChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHH---HHHHHHhCCCC--C-Ccc-hHHHHHHHHHhcCChHHHH
Q 040338          299 GPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGE---AKKLIDEMPSK--P-TCV-IWGALLGACCSHYNTKLAE  369 (385)
Q Consensus       299 ~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~---A~~~~~~m~~~--p-~~~-~~~~li~~~~~~g~~~~a~  369 (385)
                      ..+..+.+-+......+.  ..+-..+..++.++....+   ++.++++....  | ... ..-.|.-++.+.|++++|.
T Consensus        15 ~~l~~~~~~y~~e~~~~~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~   94 (126)
T 1nzn_A           15 EDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKAL   94 (126)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHH
Confidence            345566666666655454  5555557778888877666   88888888775  3 122 3334667889999999999


Q ss_pred             HHHHHHHhccccC
Q 040338          370 LVMRNLLQLDVKV  382 (385)
Q Consensus       370 ~~~~~~~~~~~~~  382 (385)
                      +.++.+++..|.+
T Consensus        95 ~~~~~lL~~eP~n  107 (126)
T 1nzn_A           95 KYVRGLLQTEPQN  107 (126)
T ss_dssp             HHHHHHHHHCTTC
T ss_pred             HHHHHHHHhCCCC
Confidence            9999999988865

>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=92.80  E-value=1  Score=39.82  Aligned_cols=32  Identities=13%  Similarity=0.072  Sum_probs=19.1

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHh
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKF   81 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~   81 (385)
                      ..|..++.........|+.+.+...+.+....
T Consensus       113 ~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L  144 (388)
T 2ff4_A          113 GRFVAEKTAGVHAAAAGRFEQASRHLSAALRE  144 (388)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence            34555555433323357788888888777664

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.76  E-value=0.71  Score=41.62  Aligned_cols=50  Identities=12%  Similarity=-0.072  Sum_probs=32.9

Q ss_pred             CCchHHHHHHHHHHHC-----CCCCCHhhHHHHHHHhcCccCccchhhHHHHHHH
Q 040338          154 GFGFETLCTFIELWNH-----GFGLSSMLYATAFSARASVYDLEWGPHLHSRVVH  203 (385)
Q Consensus       154 ~~~~~a~~~~~~m~~~-----g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~  203 (385)
                      |++++|++.+-.+.+.     +...+......++..|...++++...+.+..+.+
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lsk   84 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSK   84 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            5677777777666542     2344556677788888888888777666655544

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=92.58  E-value=0.77  Score=38.37  Aligned_cols=94  Identities=10%  Similarity=-0.044  Sum_probs=70.1

Q ss_pred             ChHHHHHHHHHHHHhccCCC---chHHHhHHHHHHh-----cCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC
Q 040338           67 NIKMALHLHGLVKKFYFVSD---ESIAKSSIDMHVK-----CGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER  138 (385)
Q Consensus        67 ~~~~a~~~~~~m~~~g~~~~---~~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~  138 (385)
                      ....|...+++..+.  .|+   -..|..|...|..     -|+.++|.+.|++..+.++                  ..
T Consensus       178 ~l~~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP------------------~~  237 (301)
T 3u64_A          178 TVHAAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCS------------------AH  237 (301)
T ss_dssp             HHHHHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCC------------------TT
T ss_pred             hHHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCC------------------CC
Confidence            355666666666664  555   5688999999998     4999999999988876552                  23


Q ss_pred             CcchHHHHHHHHHhC-CCchHHHHHHHHHHHCCCC--CCHhhHHH
Q 040338          139 DLVSWNTMISILTRH-GFGFETLCTFIELWNHGFG--LSSMLYAT  180 (385)
Q Consensus       139 ~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~g~~--p~~~t~~~  180 (385)
                      +..++......+++. |+.+++.+.+++.......  |+....+.
T Consensus       238 ~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan~  282 (301)
T 3u64_A          238 DPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVI  282 (301)
T ss_dssp             CSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHHH
T ss_pred             CchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHHH
Confidence            477888888888885 8999999999999887655  55444333

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=91.34  E-value=1  Score=32.34  Aligned_cols=87  Identities=9%  Similarity=-0.213  Sum_probs=57.1

Q ss_pred             CChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhH---HHHHHHhccCCCccccccchHHHHHHhcCCCCC--Cc
Q 040338           66 GNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDY---AESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER--DL  140 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~---a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~--~~  140 (385)
                      ..+..+.+-+......|. ++..+-..+..++.+..+..+   ++.+++...+.+                   .|  ..
T Consensus        15 ~~l~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-------------------~p~~~R   74 (126)
T 1nzn_A           15 EDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-------------------SKEEQR   74 (126)
T ss_dssp             HHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-------------------CHHHHH
T ss_pred             HHHHHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-------------------CcchHH
Confidence            444555666665555553 677777777788888776555   778887776544                   12  22


Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCC
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLS  174 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  174 (385)
                      ...-.|.-++.+.|++++|.+.++.+.+.  .|+
T Consensus        75 d~lY~LAvg~yklg~Y~~A~~~~~~lL~~--eP~  106 (126)
T 1nzn_A           75 DYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQ  106 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHh--CCC
Confidence            33334556778888888888888888874  563

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=89.92  E-value=8.1  Score=39.52  Aligned_cols=166  Identities=10%  Similarity=0.001  Sum_probs=93.5

Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCCCH-----------------------hhHHHHHHHhcCccCccchhhHHHH
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGLSS-----------------------MLYATAFSARASVYDLEWGPHLHSR  200 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-----------------------~t~~~ll~~~~~~~~~~~a~~~~~~  200 (385)
                      -.+..+|...|++++|...|.+.- .|+..+.                       .=|..++..+.+.+.++.+.++-..
T Consensus       846 yl~g~~~L~~ge~~~A~~~F~kaa-~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~l  924 (1139)
T 4fhn_B          846 YLKALIYLKSKEAVKAVRCFKTTS-LVLYSHTSQFAVLREFQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLL  924 (1139)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTCC-CSCTTCCCSCSSHHHHHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHh-hhhcccchhhhhhcccccccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            345567888899999999997642 1221110                       1134444455555555555555444


Q ss_pred             HHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCC--hhhHHHHHHHHHhcCC
Q 040338          201 VVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRN--MISWMVLISAFSQAGV  278 (385)
Q Consensus       201 ~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~--~~~~~~li~~~~~~g~  278 (385)
                      .++...+.+.                  ......|..+.+.+...|++++|...+-.++.+.  ......|+..+|..|.
T Consensus       925 Ai~~~~~~~~------------------~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r~~cLr~LV~~lce~~~  986 (1139)
T 4fhn_B          925 ADASKETDDE------------------DLSIAITHETLKTACAAGKFDAAHVALMVLSTTPLKKSCLLDFVNQLTKQGK  986 (1139)
T ss_dssp             HHHHCCSCCH------------------HHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSCHHHHHHHHHHHHHHCC
T ss_pred             HHHhccCCCh------------------hhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCC
Confidence            4433211111                  1122356778888888889999988888776543  3567778888888776


Q ss_pred             CCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhcc-c----hhhHHHHHHHHHccCCHHHHHH
Q 040338          279 LEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFT-Y----TCYFVCMVDLLGLSGLLGEAKK  338 (385)
Q Consensus       279 ~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~----~~~~~~li~~~~~~g~~~~A~~  338 (385)
                      .+.-..          +--.|..++..+++..-.+.. .    +..|..|=.-+...|++-.|-.
T Consensus       987 ~~~L~~----------lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~ 1041 (1139)
T 4fhn_B          987 INQLLN----------YSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAA 1041 (1139)
T ss_dssp             HHHHHH----------HTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHH
T ss_pred             hhhhhC----------CCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHH
Confidence            443221          223555666666665433322 1    3445555555566666554433

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=89.23  E-value=2  Score=31.79  Aligned_cols=58  Identities=7%  Similarity=-0.149  Sum_probs=44.1

Q ss_pred             CCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchH
Q 040338          153 HGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVF  211 (385)
Q Consensus       153 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  211 (385)
                      .+++++|.++|+.+.+.+-+. ...+......=.+.|++..|.+++...+..+..|...
T Consensus        73 i~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~~  130 (161)
T 4h7y_A           73 IQEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEM  130 (161)
T ss_dssp             HHCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHHH
T ss_pred             hcCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHHH
Confidence            378999999999997763333 5555555555678999999999999999988765543

>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=87.21  E-value=2.4  Score=28.90  Aligned_cols=63  Identities=11%  Similarity=-0.041  Sum_probs=47.1

Q ss_pred             CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHH
Q 040338          155 FGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLID  218 (385)
Q Consensus       155 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  218 (385)
                      +.-+..+-++.+....+.|+.......+++|.|.+|+..|.++++-++..-- +...+|.-++.
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~-~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG-PHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT-TCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc-CchhhHHHHHH
Confidence            3446667777777788999999999999999999999999999998877632 22445544443

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=87.14  E-value=7.5  Score=28.82  Aligned_cols=114  Identities=7%  Similarity=-0.104  Sum_probs=76.0

Q ss_pred             CCChhhHHHHHHHHHhhhccCCh------HHHHHHHHHHHHhccCCCch-HHHhHHHH------HHhcCChhHHHHHHHh
Q 040338           46 PRYLFTYNTMINGGVRCLCVGNI------KMALHLHGLVKKFYFVSDES-IAKSSIDM------HVKCGAVDYAESAFLR  112 (385)
Q Consensus        46 ~~~~~~~~~li~~~~~~~~~~~~------~~a~~~~~~m~~~g~~~~~~-~~~~li~~------~~~~g~~~~a~~~~~~  112 (385)
                      ..|..+|=..+..+-+   .|++      ++..++|+..... ++|+.. .|...|..      +-..+++++|.++|+.
T Consensus        10 p~~yd~W~~yl~llE~---~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~   85 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEK---NSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQM   85 (161)
T ss_dssp             CCSHHHHHHHHHHHHH---HTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH---cCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            5577788888887666   6888      8888999988875 566531 12222211      1234788999999987


Q ss_pred             ccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040338          113 MLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS  183 (385)
Q Consensus       113 m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  183 (385)
                      +.+. .              +   +- ...|-.....=.+.|+...|.+++......+.+|. ..+.+.+.
T Consensus        86 a~~~-h--------------K---kF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~-~~le~a~~  136 (161)
T 4h7y_A           86 ARAN-C--------------K---KF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPL-EMLEIALR  136 (161)
T ss_dssp             HHHH-C--------------T---TB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCH-HHHHHHHH
T ss_pred             HHHH-h--------------H---HH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcH-HHHHHHHH
Confidence            7542 1              1   12 45666666666889999999999999998776654 34444443

>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=86.99  E-value=1.9  Score=37.95  Aligned_cols=70  Identities=9%  Similarity=-0.098  Sum_probs=58.3

Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHH-----hCCCCchHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVH-----MEPSLDVFVG  213 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  213 (385)
                      ...++..+...|++++++..++.+... -+.+...+..++.++.+.|+..+|.+.|+.+.+     .|+.|+..+-
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            345667788899999999999998764 344888999999999999999999999998765     4888887654

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=86.49  E-value=5.4  Score=30.07  Aligned_cols=119  Identities=8%  Similarity=-0.080  Sum_probs=73.0

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHCC-CCCC-------HhhHHHHHHHhcCccCccchhhHHHHHHHhCC--CCchH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNHG-FGLS-------SMLYATAFSARASVYDLEWGPHLHSRVVHMEP--SLDVF  211 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~-------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~  211 (385)
                      ++-.=+..+...+.++.|+-+.+.+.... ..|+       ..++..+..++...+++..|...|++.++..-  .-+..
T Consensus        22 ~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s  101 (167)
T 3ffl_A           22 NVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSK  101 (167)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC-----
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            34445677788899999988877764421 2333       23566778888999999999999999765421  11111


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          212 VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       212 ~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                      .++++-..-..-+..+...+...---+-.+|.+.+++++|+.+++.++.
T Consensus       102 ~~~~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~  150 (167)
T 3ffl_A          102 VRPSTGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPS  150 (167)
T ss_dssp             ---------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCG
T ss_pred             ccccccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCc
Confidence            1111110000111122344556666788999999999999999999864

>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=84.71  E-value=5.2  Score=27.23  Aligned_cols=62  Identities=6%  Similarity=-0.046  Sum_probs=48.4

Q ss_pred             hhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHH
Q 040338          103 VDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAF  182 (385)
Q Consensus       103 ~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll  182 (385)
                      .=+..+-++.+...+.                  -|++.+..+.+.+|-|.+++.-|.++|+-.+.+ +.+...+|..++
T Consensus        26 ~~e~rrglN~l~~~Dl------------------VP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~l   86 (109)
T 1v54_E           26 AWELRKGMNTLVGYDL------------------VPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVI   86 (109)
T ss_dssp             HHHHHHHHHHHTTSSB------------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHhcccc------------------CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHH
Confidence            3355566666666666                  699999999999999999999999999998775 444455677776


Q ss_pred             H
Q 040338          183 S  183 (385)
Q Consensus       183 ~  183 (385)
                      .
T Consensus        87 q   87 (109)
T 1v54_E           87 Q   87 (109)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=84.46  E-value=3.6  Score=27.85  Aligned_cols=87  Identities=15%  Similarity=0.055  Sum_probs=55.9

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHH--HHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcch
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSI--DMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVS  142 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li--~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~  142 (385)
                      .+..++|.-+-+.+...|   + .-.-.+|  ..+...|++++|..+.+.+                      ..||...
T Consensus        19 ~H~HqEA~tIAdwL~~~~---~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----------------------c~pdlep   72 (115)
T 2uwj_G           19 QHCHEEALCIAEWLERLG---Q-DEAARLIRISSLANQGRYQEALAFAHGN----------------------PWPALEP   72 (115)
T ss_dssp             TTCHHHHHHHHHHHHHTT---C-HHHHHHHHHHHHHHTTCHHHHHGGGTTC----------------------CCGGGHH
T ss_pred             chHHHHHHHHHHHHHhCC---c-HHHHHHHHHHHHHcchhHHHHHHhcCCC----------------------CCchHHH
Confidence            466777777777777654   2 2223333  4455677777777766433                      3688888


Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYAT  180 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~  180 (385)
                      |-+|-.  .+.|-.+++...+.++...| .|....|..
T Consensus        73 w~ALce--~rlGl~s~le~rL~~la~sg-~p~~q~Fa~  107 (115)
T 2uwj_G           73 WFALCE--WHLGLGAALDRRLAGLGGSS-DPALADFAA  107 (115)
T ss_dssp             HHHHHH--HHTTCHHHHHHHHHHHHTCS-SHHHHHHHH
T ss_pred             HHHHHH--HhcccHHHHHHHHHHHHhCC-CHHHHHHHH
Confidence            877654  47788888888887777664 444555543

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=84.41  E-value=27  Score=32.79  Aligned_cols=106  Identities=9%  Similarity=-0.052  Sum_probs=62.0

Q ss_pred             HHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCCC-C-
Q 040338          272 AFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKP-T-  348 (385)
Q Consensus       272 ~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p-~-  348 (385)
                      ...+...+..+.....+..+.......+...++...+........ .....-.+....+.|+++.|...|+.|...+ + 
T Consensus       239 ~~~~~~~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~r~Alr~~d~~~a~~~~~~l~~~~~~~  318 (618)
T 1qsa_A          239 SLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEK  318 (618)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTTGGGS
T ss_pred             hhhhccCCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhccccCCChHHHHHHHHHHHHCCCHHHHHHHHHHcccccccc
Confidence            333334444444433555555556666634455555555433322 2223333444456799999999999998752 2 


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040338          349 CVIWGALLGACCSHYNTKLAELVMRNLLQ  377 (385)
Q Consensus       349 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~  377 (385)
                      ..-.--+..++...|+.++|..+|+++.+
T Consensus       319 ~r~~YW~~ra~~~~g~~~~a~~~~~~~a~  347 (618)
T 1qsa_A          319 DEWRYWQADLLLERGREAEAKEILHQLMQ  347 (618)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HhHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            22223355677788999999999888764

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=84.11  E-value=15  Score=35.43  Aligned_cols=130  Identities=10%  Similarity=-0.023  Sum_probs=75.2

Q ss_pred             HHHHHHHHhCCC-chHHHHHHHHHHHCCCCCCHhhH--HHHHHHhcCccC-ccchhhHHHHHHHh------CCCCchHHH
Q 040338          144 NTMISILTRHGF-GFETLCTFIELWNHGFGLSSMLY--ATAFSARASVYD-LEWGPHLHSRVVHM------EPSLDVFVG  213 (385)
Q Consensus       144 ~~li~~~~~~~~-~~~a~~~~~~m~~~g~~p~~~t~--~~ll~~~~~~~~-~~~a~~~~~~~~~~------~~~~~~~~~  213 (385)
                      ..|+..+...++ .+.|.++|+++...  .|...++  ..++..+...++ --+|.+++.+.++.      ...+.....
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~--~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKK--DPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhh--CCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            445556666666 57899999999886  4433332  233443333332 22355555554431      111111111


Q ss_pred             HHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH
Q 040338          214 SGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF  286 (385)
Q Consensus       214 ~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~  286 (385)
                      ..++..           +....+.-.+.+...|+++.|+.+-++...  | +-.+|..|..+|...|+++.|+-.+
T Consensus       330 ~~~~~~-----------~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtL  394 (754)
T 4gns_B          330 ARLMNC-----------MSDLLNIQTNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAI  394 (754)
T ss_dssp             HHHHHH-----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ccccCc-----------chHHHHHHHHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHH
Confidence            111100           111222334556678899999999887765  5 5689999999999999999998777

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.54  E-value=24  Score=31.55  Aligned_cols=180  Identities=14%  Similarity=0.091  Sum_probs=107.3

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHC-CCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNH-GFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      ........++..|...++++...+.+..+.+. |..+...  ..+++.+.         ..+.    .-..++..+.-.+
T Consensus        54 s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai--~~~V~~~~---------~~l~----~~~~~d~~~~~~~  118 (445)
T 4b4t_P           54 SSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSI--QYMIQKVM---------EYLK----SSKSLDLNTRISV  118 (445)
T ss_dssp             TCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHH--HHHHHHHH---------HHHH----HHCTTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHH--HHHHHHHH---------HHHh----cCCchhHHHHHHH
Confidence            34556777889999999999988877766543 3222222  22332221         1111    1122344444444


Q ss_pred             HHHHHhc--CCCCCC-chhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q 040338          217 IDMYLKC--GCNGIE-SSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLS  293 (385)
Q Consensus       217 i~~~~~~--g~~~~~-~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~  293 (385)
                      +......  |..-+. ........|...|-..|++.+|..++..+...   |+          |..+....+-.+...+.
T Consensus       119 i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~E---t~----------~~~~~~~kve~~l~q~r  185 (445)
T 4b4t_P          119 IETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVE---TY----------GSMEMSEKIQFILEQME  185 (445)
T ss_dssp             HHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---HC----------SSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH---HH----------hcccHHHHHHHHHHHHH
Confidence            4433221  111111 12334456778888899999999999888621   11          22233333335666777


Q ss_pred             HhcccCChhhHHHHHHHHHhccc---------hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          294 GCSHSGPVTKGKHYFTAMAKFTY---------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       294 ~~~~~~~~~~a~~~~~~~~~~~~---------~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      .|...+++.+|..+..++.....         ...+...+..+...+++.+|.+.|.+..+
T Consensus       186 l~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          186 LSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            78888888888888887653221         55667788888889999998888877654

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=83.05  E-value=23  Score=31.11  Aligned_cols=143  Identities=8%  Similarity=-0.072  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHcCCChhHHHHHHHhccc--------CChhhHHHHHHHHHhcCCCC-chHHHH------------HH----
Q 040338          234 IGKALVTMYAEGGSTQKADLAFELMSR--------RNMISWMVLISAFSQAGVLE-KPRFFF------------FF----  288 (385)
Q Consensus       234 ~~~~li~~~~~~g~~~~A~~~~~~m~~--------~~~~~~~~li~~~~~~g~~~-~a~~~~------------~~----  288 (385)
                      ....|...|.+.|+.++..+++.....        ........|++.+....+.. .-.++.            +|    
T Consensus        21 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~r~flr~~  100 (394)
T 3txn_A           21 GILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQS  100 (394)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677778888888888888877653        12234555666665543221 111111            23    


Q ss_pred             --HHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-----CCcchHH
Q 040338          289 --VSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-----PTCVIWG  353 (385)
Q Consensus       289 --~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----p~~~~~~  353 (385)
                        ..++..|...|++.+|..++..+.+.-.        ..++..-++.|...+++..+...+......     +++..-.
T Consensus       101 l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~i~a  180 (394)
T 3txn_A          101 LEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQG  180 (394)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHHHHH
Confidence              2678888999999999888888777422        677777888899999999998888766431     2222211


Q ss_pred             ----HHHHHHH-hcCChHHHHHHHHHHH
Q 040338          354 ----ALLGACC-SHYNTKLAELVMRNLL  376 (385)
Q Consensus       354 ----~li~~~~-~~g~~~~a~~~~~~~~  376 (385)
                          .-.-.+. ..+++..|...|=+..
T Consensus       181 ~i~~~~Gi~~l~~~rdyk~A~~~F~eaf  208 (394)
T 3txn_A          181 ALDLQSGILHAADERDFKTAFSYFYEAF  208 (394)
T ss_dssp             HHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHhccCHHHHHHHHHHHH
Confidence                1122245 6788988888776653

>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=82.80  E-value=3.8  Score=27.80  Aligned_cols=87  Identities=14%  Similarity=0.035  Sum_probs=56.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHH--HHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcch
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSI--DMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVS  142 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li--~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~  142 (385)
                      .+..++|.-+-+.+...|   + .-.-.+|  ..+...|++++|..+.+.+.                      .||...
T Consensus        20 ~H~HqEA~tIAdwL~~~~---~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c----------------------~pdlep   73 (116)
T 2p58_C           20 NHYHEEANCIAEWLHLKG---E-EEAVQLIRLSSLMNRGDYASALQQGNKLA----------------------YPDLEP   73 (116)
T ss_dssp             TTCHHHHHHHHHHHHHTT---C-HHHHHHHHHHHHHHTTCHHHHHHHHTTSC----------------------CGGGHH
T ss_pred             chHHHHHHHHHHHHHhCC---c-HHHHHHHHHHHHHcchhHHHHHHhcCCCC----------------------CchHHH
Confidence            466778888887777654   2 2223344  45566788888888775443                      588888


Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHH
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYAT  180 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~  180 (385)
                      |-+|-..  +.|-.+++...+.++...| .|....|..
T Consensus        74 w~ALce~--rlGl~s~le~rL~~la~sg-~p~~q~Fa~  108 (116)
T 2p58_C           74 WLALCEY--RLGLGSALESRLNRLARSQ-DPRIQTFVN  108 (116)
T ss_dssp             HHHHHHH--HHTCHHHHHHHHHHHTTCC-CHHHHHHHH
T ss_pred             HHHHHHH--hcccHHHHHHHHHHHHhCC-CHHHHHHHH
Confidence            8776543  6777778877777776554 444445443

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=80.92  E-value=5.4  Score=28.82  Aligned_cols=59  Identities=12%  Similarity=-0.035  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          158 ETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       158 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      +..+-++.+...++.|+.......+++|-+.+|+..|.++++-++..- .+...+|.-++
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~l  129 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI  129 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHH
Confidence            455666666677788888888888888888888888888888887653 22244454443

---

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	385
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.84
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.77
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.46
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.43
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.05
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.99
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.96
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.94
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.92
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.86
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.84
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.74
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.7
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.69
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.56
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.54
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.37
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.29
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.29
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.21
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.19
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.16
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.13
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.12
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.05
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.02
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.0
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.97
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.95
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.94
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.82
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.75
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.74
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.68
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.58
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.49
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.43
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.42
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.4
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.4
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.4
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.28
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.19
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.17
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.16
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.14
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.09
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.05
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.92
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.65
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.64
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.35
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.34
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.86
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.69
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.28
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	94.9
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	92.96
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	91.55
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	89.91
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	88.36
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	85.33
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	85.19

>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=99.84  E-value=6.1e-18  Score=149.47  Aligned_cols=307  Identities=9%  Similarity=0.033  Sum_probs=212.3

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccc-----
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWK-----  122 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~-----  122 (385)
                      ++..+..+...+..   .|++++|...++...+.. +-+..++..+..+|.+.|++++|...+....+.+.....     
T Consensus        32 ~~~~~~~la~~~~~---~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  107 (388)
T d1w3ba_          32 NTGVLLLLSSIHFQ---CRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINL  107 (388)
T ss_dssp             CHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccccccccccccccccccccccccccc
Confidence            45566666666555   788888888888888764 335677888888888888888888888777554332111     


Q ss_pred             -------cchHHHHHH---hcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCcc
Q 040338          123 -------FGIIRLLIM---FQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLE  192 (385)
Q Consensus       123 -------~~~~~a~~~---~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~  192 (385)
                             +....+...   ......................+....+...+....... +-+...+..+...+...|+++
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~  186 (388)
T d1w3ba_         108 AAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIW  186 (388)
T ss_dssp             HHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccC-cchhHHHHhhcccccccCcHH
Confidence                   000000000   001112333344445555566666667776666665541 224556666677777778888


Q ss_pred             chhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHH
Q 040338          193 WGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVL  269 (385)
Q Consensus       193 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~l  269 (385)
                      +|...++...+..+                       .+..++..+...+...|++++|...++...+   .+...+..+
T Consensus       187 ~A~~~~~~al~~~p-----------------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l  243 (388)
T d1w3ba_         187 LAIHHFEKAVTLDP-----------------------NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNL  243 (388)
T ss_dssp             HHHHHHHHHHHHCT-----------------------TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCc-----------------------ccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHH
Confidence            88888777766532                       1233445666667777778888877776654   345566667


Q ss_pred             HHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHH
Q 040338          270 ISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGE  335 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~  335 (385)
                      ...+.+.|++++|+..+            ++..+...+...|++++|.+.++......+  ...+..+...+.+.|++++
T Consensus       244 ~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  323 (388)
T d1w3ba_         244 ACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEE  323 (388)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHH
Confidence            77777788888777777            677778888888888999999988887776  7777888888999999999


Q ss_pred             HHHHHHhCCCC-CC-cchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          336 AKKLIDEMPSK-PT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       336 A~~~~~~m~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      |++.|++..+. |+ ..+|..+...|...|++++|...+++.++.+|..
T Consensus       324 A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~  372 (388)
T d1w3ba_         324 AVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTF  372 (388)
T ss_dssp             HHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTC
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence            99999987763 54 5578888899999999999999999998887764

>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=99.77  E-value=1.9e-16  Score=139.63  Aligned_cols=296  Identities=11%  Similarity=0.041  Sum_probs=233.7

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|.+.++++.+.. +-+...+..+..+|.+.|++++|...|++..+.+                   +.+..+|.
T Consensus        12 ~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~a~~   71 (388)
T d1w3ba_          12 AGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-------------------PLLAEAYS   71 (388)
T ss_dssp             HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHH
Confidence            699999999999998874 3367888999999999999999999999876655                   35677899


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCG  224 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  224 (385)
                      .+..+|.+.|++++|+..+....+... .+..............+....+................... .........+
T Consensus        72 ~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  149 (388)
T d1w3ba_          72 NLGNVYKERGQLQEAIEHYRHALRLKP-DFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRS-DLGNLLKALG  149 (388)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHH-HHHHHHHTTS
T ss_pred             HHHHHhhhhcccccccccccccccccc-ccccccccccccccccccccccccccccccccccccccccc-cccccccccc
Confidence            999999999999999999999987632 33444444444555556666666555555554433322222 2222222222


Q ss_pred             CCC------------CCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHH---
Q 040338          225 CNG------------IESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFF---  286 (385)
Q Consensus       225 ~~~------------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~---  286 (385)
                      ...            .+.+...+..+...+...|++++|...+++..+  | +...+..+...+...|++++|+..+   
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  229 (388)
T d1w3ba_         150 RLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRA  229 (388)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             hhhhhHHHHHHhhccCcchhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHh
Confidence            111            334467778888999999999999999998765  3 5678889999999999999999988   


Q ss_pred             ---------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHH
Q 040338          287 ---------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWG  353 (385)
Q Consensus       287 ---------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~  353 (385)
                               .+..+...+.+.|++++|...+++..+..+  ...+..+...+...|++++|.+.++.....  .+...+.
T Consensus       230 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  309 (388)
T d1w3ba_         230 LSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLN  309 (388)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhh
Confidence                     777888999999999999999999988877  788889999999999999999999887653  4567888


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          354 ALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       354 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .+...+...|++++|+..+++.++..|..
T Consensus       310 ~l~~~~~~~~~~~~A~~~~~~al~~~p~~  338 (388)
T d1w3ba_         310 NLANIKREQGNIEEAVRLYRKALEVFPEF  338 (388)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHTTSCTTC
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            89999999999999999999999888764

>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=99.46  E-value=1.9e-12  Score=111.19  Aligned_cols=242  Identities=12%  Similarity=-0.012  Sum_probs=164.5

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...|+.+.+.. +-+..+|..+..+|...|++++|...|++..+.+                   +.+...|.
T Consensus        32 ~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~~~~   91 (323)
T d1fcha_          32 EGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-------------------PDNQTALM   91 (323)
T ss_dssp             TTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-------------------cccccccc
Confidence            799999999999999864 3367889999999999999999999998876544                   34677888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHH----------------HHHHHhcCccCccchhhHHHHHHHhCCCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYA----------------TAFSARASVYDLEWGPHLHSRVVHMEPSL  208 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~----------------~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  208 (385)
                      .+...|...|++++|.+.+++....  .|+.....                ..+..+...+...++.+.+....+..+. 
T Consensus        92 ~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~-  168 (323)
T d1fcha_          92 ALAVSFTNESLQRQACEILRDWLRY--TPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPT-  168 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHT--STTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTT-
T ss_pred             cccccccccccccccccchhhHHHh--ccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhc-
Confidence            8999999999999999999998764  33321110                0111112223344445555544443221 


Q ss_pred             chHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHH
Q 040338          209 DVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFF  285 (385)
Q Consensus       209 ~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~  285 (385)
                                          ..+..++..+...+...|++++|+..|++..+  | +...|..+                
T Consensus       169 --------------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l----------------  212 (323)
T d1fcha_         169 --------------------SIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKL----------------  212 (323)
T ss_dssp             --------------------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH----------------
T ss_pred             --------------------ccccccchhhHHHHHHHHHHhhhhcccccccccccccccchhhh----------------
Confidence                                12344556677777888888888888887654  2 23344444                


Q ss_pred             HHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C------------Ccc
Q 040338          286 FFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P------------TCV  350 (385)
Q Consensus       286 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p------------~~~  350 (385)
                            ...+...|++++|.+.+++..+..+  ...+..+..+|.+.|++++|++.|++..+- |            ...
T Consensus       213 ------g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~  286 (323)
T d1fcha_         213 ------GATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSEN  286 (323)
T ss_dssp             ------HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHH
T ss_pred             ------hhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHH
Confidence                  4445555666677777777776655  777788888888999999998888876541 1            112


Q ss_pred             hHHHHHHHHHhcCChHHHHHH
Q 040338          351 IWGALLGACCSHYNTKLAELV  371 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~  371 (385)
                      .|..+-.++...|+.+.+...
T Consensus       287 ~~~~l~~al~~~~~~d~~~~~  307 (323)
T d1fcha_         287 IWSTLRLALSMLGQSDAYGAA  307 (323)
T ss_dssp             HHHHHHHHHHHHTCGGGHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHH
Confidence            466666777777766655433

>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=99.43  E-value=1.1e-12  Score=112.81  Aligned_cols=214  Identities=12%  Similarity=-0.029  Sum_probs=163.2

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKC  223 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  223 (385)
                      -....+.+.|++++|+..|++..+.  .| +..+|..+..++...|++++|...+++.++..+.                
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~----------------   85 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPD----------------   85 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccc----------------
Confidence            3455678899999999999999885  45 5778888889999999999999999998886532                


Q ss_pred             CCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc--CCh----------------hhHHHHHHHHHhcCCCCchHHH
Q 040338          224 GCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR--RNM----------------ISWMVLISAFSQAGVLEKPRFF  285 (385)
Q Consensus       224 g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~----------------~~~~~li~~~~~~g~~~~a~~~  285 (385)
                             +...+..+...|...|++++|.+.++....  |+.                ......+..+...+...++.+.
T Consensus        86 -------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  158 (323)
T d1fcha_          86 -------NQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKEL  158 (323)
T ss_dssp             -------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHH
T ss_pred             -------cccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHH
Confidence                   233456667777888899999999887754  110                0000111122222333333333


Q ss_pred             H--------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CC-
Q 040338          286 F--------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-  347 (385)
Q Consensus       286 ~--------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-  347 (385)
                      +              .+..+...+...|++++|...+++.....+  ...+..+...|.+.|++++|.+.|++..+ .| 
T Consensus       159 ~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~  238 (323)
T d1fcha_         159 FLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPG  238 (323)
T ss_dssp             HHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHHhhc
Confidence            3              566777888899999999999999988777  88888999999999999999999998765 34 


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          348 TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       348 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      +..+|..+..+|.+.|++++|+..|++.++..|...
T Consensus       239 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~  274 (323)
T d1fcha_         239 YIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSR  274 (323)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC-
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCh
Confidence            466799999999999999999999999998877654

>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=99.05  E-value=5e-09  Score=90.04  Aligned_cols=257  Identities=11%  Similarity=-0.022  Sum_probs=179.4

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCC----cchHHHHHHHHHhCCCchHHHHHHHH
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERD----LVSWNTMISILTRHGFGFETLCTFIE  165 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~  165 (385)
                      .......+...|++++|++++++..+...                  ..+    ..+++.+...+...|++++|+..|++
T Consensus        15 ~~lrA~~~~~~g~~~~A~~~~~~aL~~~~------------------~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~   76 (366)
T d1hz4a_          15 NALRAQVAINDGNPDEAERLAKLALEELP------------------PGWFYSRIVATSVLGEVLHCKGELTRSLALMQQ   76 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCC------------------TTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCc------------------CCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            33345667789999999999987654331                  111    34677788899999999999999998


Q ss_pred             HHHCC----CCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHH
Q 040338          166 LWNHG----FGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVT  240 (385)
Q Consensus       166 m~~~g----~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~  240 (385)
                      ..+..    ..+ ...++..+...+...|++..+...+........               ..+..........+..+..
T Consensus        77 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~---------------~~~~~~~~~~~~~~~~la~  141 (366)
T d1hz4a_          77 TEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLIN---------------EQHLEQLPMHEFLVRIRAQ  141 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH---------------HTTCTTSTHHHHHHHHHHH
T ss_pred             HHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH---------------hcccchhhHHHHHHHHHHH
Confidence            86531    111 234556667778888999999988887664311               0000001111234455667


Q ss_pred             HHHcCCChhHHHHHHHhccc--------CChhhHHHHHHHHHhcCCCCchHHHH-------------------HHHHHHH
Q 040338          241 MYAEGGSTQKADLAFELMSR--------RNMISWMVLISAFSQAGVLEKPRFFF-------------------FFVSLLS  293 (385)
Q Consensus       241 ~~~~~g~~~~A~~~~~~m~~--------~~~~~~~~li~~~~~~g~~~~a~~~~-------------------~~~~l~~  293 (385)
                      .+...|+++.+...+....+        .....+..+...+...+...++...+                   .+.....
T Consensus       142 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  221 (366)
T d1hz4a_         142 LLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVI  221 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHH
T ss_pred             HHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHH
Confidence            77888899999988887754        12244555566667777777766665                   5666777


Q ss_pred             HhcccCChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHHHhCCC-------CC-CcchHHHHHHHH
Q 040338          294 GCSHSGPVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-------KP-TCVIWGALLGAC  359 (385)
Q Consensus       294 ~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------~p-~~~~~~~li~~~  359 (385)
                      .+...|+.+.|...++.......      ...+..+...+...|++++|.+.++....       .| ...++..+...|
T Consensus       222 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~  301 (366)
T d1hz4a_         222 YWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLY  301 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHH
Confidence            78889999999999988766544      34455678889999999999999987753       12 245677888999


Q ss_pred             HhcCChHHHHHHHHHHHhcc
Q 040338          360 CSHYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       360 ~~~g~~~~a~~~~~~~~~~~  379 (385)
                      ...|++++|.+.+++.++..
T Consensus       302 ~~~g~~~~A~~~l~~Al~l~  321 (366)
T d1hz4a_         302 WQAGRKSDAQRVLLDALKLA  321 (366)
T ss_dssp             HHHTCHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHh
Confidence            99999999999999877643

>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=98.99  E-value=5.7e-08  Score=83.20  Aligned_cols=273  Identities=10%  Similarity=-0.031  Sum_probs=173.2

Q ss_pred             cCChHHHHHHHHHHHHhccCCC----chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC--C
Q 040338           65 VGNIKMALHLHGLVKKFYFVSD----ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE--R  138 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~--~  138 (385)
                      .|++++|++++++..+.....+    ...+..+..+|...|++++|.+.|++..+..               .....  .
T Consensus        25 ~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~---------------~~~~~~~~   89 (366)
T d1hz4a_          25 DGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMA---------------RQHDVWHY   89 (366)
T ss_dssp             TTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH---------------HHTTCHHH
T ss_pred             CCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH---------------HhhcchHH
Confidence            7999999999999887532211    2356677788889999999999997764321               11111  1


Q ss_pred             CcchHHHHHHHHHhCCCchHHHHHHHHHHHC----CCC--CC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchH
Q 040338          139 DLVSWNTMISILTRHGFGFETLCTFIELWNH----GFG--LS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVF  211 (385)
Q Consensus       139 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~--p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  211 (385)
                      ....+..+...+...|++..+...+.+....    +..  +. ...+..+...+...|+++.+...+.............
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  169 (366)
T d1hz4a_          90 ALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQ  169 (366)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhh
Confidence            2335566777888899999999888876532    211  11 2345556677888899999999888887764332211


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc-----C-----ChhhHHHHHHHHHhcCCCCc
Q 040338          212 VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR-----R-----NMISWMVLISAFSQAGVLEK  281 (385)
Q Consensus       212 ~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----~-----~~~~~~~li~~~~~~g~~~~  281 (385)
                                        .....+..+...+...++...+...+.....     .     ....+..+...+...|++++
T Consensus       170 ------------------~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  231 (366)
T d1hz4a_         170 ------------------QQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAA  231 (366)
T ss_dssp             ------------------GGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             ------------------hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHH
Confidence                              1112223334444555566655555544332     0     11234444555666666666


Q ss_pred             hHHHH----------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHH
Q 040338          282 PRFFF----------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAK  337 (385)
Q Consensus       282 a~~~~----------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~  337 (385)
                      |...+                .+..+..++...|++++|...++.......        ...+..+...|.+.|++++|.
T Consensus       232 a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  311 (366)
T d1hz4a_         232 AANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQ  311 (366)
T ss_dssp             HHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHH
Confidence            66665                455667777888888888888887764322        567777889999999999999


Q ss_pred             HHHHhCCCC----C-------CcchHHHHHHHHHhcCChHHHHH
Q 040338          338 KLIDEMPSK----P-------TCVIWGALLGACCSHYNTKLAEL  370 (385)
Q Consensus       338 ~~~~~m~~~----p-------~~~~~~~li~~~~~~g~~~~a~~  370 (385)
                      +.+++..+-    .       .......++..+...+..+++.+
T Consensus       312 ~~l~~Al~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~e~e~  355 (366)
T d1hz4a_         312 RVLLDALKLANRTGFISHFVIEGEAMAQQLRQLIQLNTLPELEQ  355 (366)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHTTHHHHHHHHHHHHHTTCSCHHHH
T ss_pred             HHHHHHHHHhhhcCcHHHHHHHHHHHHHHHHHHHhcCCChHHHH
Confidence            999876541    1       11234445666666676666544

>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=98.96  E-value=8.2e-09  Score=88.51  Aligned_cols=249  Identities=9%  Similarity=-0.047  Sum_probs=176.3

Q ss_pred             HhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHH----------HHhCCCchHHH
Q 040338           91 KSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISI----------LTRHGFGFETL  160 (385)
Q Consensus        91 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~----------~~~~~~~~~a~  160 (385)
                      ..++......+..++|++++++..+.+                   +-+...|+..-..          +...|++++|+
T Consensus        33 ~~~~~~~~~~~~~~~al~~~~~~l~~~-------------------P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al   93 (334)
T d1dcea1          33 QAVFQKRQAGELDESVLELTSQILGAN-------------------PDFATLWNCRREVLQHLETEKSPEESAALVKAEL   93 (334)
T ss_dssp             HHHHHHHHTTCCSHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHC-------------------CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHH
Confidence            334443433444589999998876544                   2233455443222          23345578899


Q ss_pred             HHHHHHHHCCCCC-CHhhHHHHHHHhcCc--cCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHH
Q 040338          161 CTFIELWNHGFGL-SSMLYATAFSARASV--YDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKA  237 (385)
Q Consensus       161 ~~~~~m~~~g~~p-~~~t~~~ll~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~  237 (385)
                      .+++...+.  .| +...+..+..++...  ++++++...++.+....+. +...+                     +..
T Consensus        94 ~~~~~~l~~--~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~-~~~~~---------------------~~~  149 (334)
T d1dcea1          94 GFLESCLRV--NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADER-NFHCW---------------------DYR  149 (334)
T ss_dssp             HHHHHHHHH--CTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTT-CHHHH---------------------HHH
T ss_pred             HHHHHHHHh--CCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCch-hhhhh---------------------hhH
Confidence            999998875  34 455555555555544  4578899999999887542 12211                     123


Q ss_pred             HHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH--------HHHHHHHHhcccCChhhHHH
Q 040338          238 LVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF--------FFVSLLSGCSHSGPVTKGKH  306 (385)
Q Consensus       238 li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~--------~~~~l~~~~~~~~~~~~a~~  306 (385)
                      ....+...+..++|+..++...+.   +...|+.+..++.+.|++++|...+        ........+...+..+++..
T Consensus       150 ~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~  229 (334)
T d1dcea1         150 RFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAW  229 (334)
T ss_dssp             HHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHH
T ss_pred             HHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHH
Confidence            345666788999999999988863   6678888999999999999887666        22334444556677788888


Q ss_pred             HHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          307 YFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       307 ~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      .+.......+  ...+..+...+...|+.++|.+.+.+.... | +..+|..+...|.+.|++++|.+.+++.++.+|..
T Consensus       230 ~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~  309 (334)
T d1dcea1         230 FYHRWLLGRAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMR  309 (334)
T ss_dssp             HHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGG
T ss_pred             HHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCccc
Confidence            8888777666  555666777888889999999999988764 4 45678889999999999999999999999998853

>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=98.94  E-value=7.3e-08  Score=81.67  Aligned_cols=214  Identities=8%  Similarity=0.009  Sum_probs=152.2

Q ss_pred             chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCC-chHHHHHHHH
Q 040338           87 ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGF-GFETLCTFIE  165 (385)
Q Consensus        87 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~  165 (385)
                      ...|+-+-..+.+.+..++|+++++++.+.+                   +-+...|+....++...|+ +++|+..+++
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-------------------P~~~~a~~~r~~~l~~l~~~~~eal~~~~~  103 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-------------------AANYTVWHFRRVLLKSLQKDLHEEMNYITA  103 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-------------------CCChHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence            3456666677888889999999998887765                   3567788888888888764 8999999999


Q ss_pred             HHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHc
Q 040338          166 LWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAE  244 (385)
Q Consensus       166 m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~  244 (385)
                      ..+.  .| +..+|..+...+.+.|++++|++.++.+++..+                       .+..+|..+...+.+
T Consensus       104 al~~--~p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~dp-----------------------~n~~a~~~~~~~~~~  158 (315)
T d2h6fa1         104 IIEE--QPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDA-----------------------KNYHAWQHRQWVIQE  158 (315)
T ss_dssp             HHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-----------------------TCHHHHHHHHHHHHH
T ss_pred             HHHH--HHhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhhh-----------------------cchHHHHHHHHHHHH
Confidence            8775  44 577888888888899999999999999988753                       244556777777788


Q ss_pred             CCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--hhh
Q 040338          245 GGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCY  319 (385)
Q Consensus       245 ~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~  319 (385)
                      .|++++|++.+++..+  | +...|+.+...+.+.+....+                +.+++|...+....+..+  ...
T Consensus       159 ~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~----------------~~~~~ai~~~~~al~~~P~~~~~  222 (315)
T d2h6fa1         159 FKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDR----------------AVLEREVQYTLEMIKLVPHNESA  222 (315)
T ss_dssp             HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSH----------------HHHHHHHHHHHHHHHHSTTCHHH
T ss_pred             HHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccchh----------------hhhHHhHHHHHHHHHhCCCchHH
Confidence            8899999999998876  3 566777777777776665443                345677777877777766  555


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhCCC-CC---CcchHHHHHHHHHh
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEMPS-KP---TCVIWGALLGACCS  361 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m~~-~p---~~~~~~~li~~~~~  361 (385)
                      +.-+...+.. ...+++.+.++...+ .|   +...+..++..|..
T Consensus       223 ~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~  267 (315)
T d2h6fa1         223 WNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYED  267 (315)
T ss_dssp             HHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHH
Confidence            5555444443 335666665554433 12   33445566666644

>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=98.92  E-value=1.2e-07  Score=80.21  Aligned_cols=176  Identities=7%  Similarity=-0.016  Sum_probs=131.2

Q ss_pred             hHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcC-ChhHHHHHHHhccCCCccccccchHHHH
Q 040338           51 TYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCG-AVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        51 ~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      .|+.+-..+.+   .+..++|+++++++++.. |-+...|+....++...| ++++|+..++...+.+            
T Consensus        45 a~~~~~~~~~~---~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~------------  108 (315)
T d2h6fa1          45 VYDYFRAVLQR---DERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ------------  108 (315)
T ss_dssp             HHHHHHHHHHH---TCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHh---CCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH------------
Confidence            34444344444   789999999999999975 336678888888888866 5899999998886655            


Q ss_pred             HHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCC
Q 040338          130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSL  208 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  208 (385)
                             +.+..+|+.+...+.+.|++++|+..++++.+.  .| +...|..+...+.+.|++++|++.++.+++..+. 
T Consensus       109 -------p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~-  178 (315)
T d2h6fa1         109 -------PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-  178 (315)
T ss_dssp             -------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-
T ss_pred             -------HhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCc-
Confidence                   467889999999999999999999999999885  44 6889999999999999999999999999998642 


Q ss_pred             chHHHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCC------hhHHHHHHHhccc--C-ChhhHHHHHHHHH
Q 040338          209 DVFVGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGS------TQKADLAFELMSR--R-NMISWMVLISAFS  274 (385)
Q Consensus       209 ~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~------~~~A~~~~~~m~~--~-~~~~~~~li~~~~  274 (385)
                      +...|                      +.+...+.+.++      +++|++.+....+  | +...|+.+...+.
T Consensus       179 n~~a~----------------------~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~  231 (315)
T d2h6fa1         179 NNSVW----------------------NQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQ  231 (315)
T ss_dssp             CHHHH----------------------HHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHT
T ss_pred             cHHHH----------------------HHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHH
Confidence            33334                      333333333333      5677777776654  3 4555655554443

>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=98.86  E-value=2.6e-07  Score=77.97  Aligned_cols=214  Identities=10%  Similarity=-0.031  Sum_probs=137.1

Q ss_pred             hHHHHHHHHHHHHhccCCCchHHHhHHHHHHhc--------------CChhHHHHHHHhccCCCccccccchHHHHHHhc
Q 040338           68 IKMALHLHGLVKKFYFVSDESIAKSSIDMHVKC--------------GAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQ  133 (385)
Q Consensus        68 ~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~--------------g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~  133 (385)
                      .+++..+|+++...- +.+...|-..+..+-+.              +..++|..+|++..+...               
T Consensus        32 ~~Rv~~vyerAl~~~-~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~---------------   95 (308)
T d2onda1          32 TKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLL---------------   95 (308)
T ss_dssp             HHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTT---------------
T ss_pred             HHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcC---------------
Confidence            345666777776652 34556665555544322              234667777766554322               


Q ss_pred             CCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHH
Q 040338          134 KMPERDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVG  213 (385)
Q Consensus       134 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  213 (385)
                         +.+...|...+....+.|+++.|..+|+++.+.........|...+..+.+.|+.+.|.++|+.+++.++.. ...|
T Consensus        96 ---p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~~-~~~~  171 (308)
T d2onda1          96 ---KKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTR-HHVY  171 (308)
T ss_dssp             ---TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCC-THHH
T ss_pred             ---CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCc-HHHH
Confidence               456667888888889999999999999998875322234467788888888899999999999887765422 2222


Q ss_pred             HHHHHHHHhcCCCCCCchhhHHHHHHH-HHHcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHH
Q 040338          214 SGLIDMYLKCGCNGIESSIQIGKALVT-MYAEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFV  289 (385)
Q Consensus       214 ~~li~~~~~~g~~~~~~~~~~~~~li~-~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~  289 (385)
                                            ..... -+...|+.+.|..+|+.+.+  | +...|...                    
T Consensus       172 ----------------------~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y--------------------  209 (308)
T d2onda1         172 ----------------------VTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAY--------------------  209 (308)
T ss_dssp             ----------------------HHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHH--------------------
T ss_pred             ----------------------HHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHH--------------------
Confidence                                  11111 12335678888888887765  2 22333333                    


Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc------hhhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                        +......|+.+.|+.+|++..+..+      ...|...+..-...|+.+.+.++++++.+
T Consensus       210 --~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         210 --IDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             --HHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             --HHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              3333455667777777887766543      34677777777778888888888877643

>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=98.84  E-value=2.8e-07  Score=77.77  Aligned_cols=208  Identities=7%  Similarity=-0.056  Sum_probs=135.0

Q ss_pred             hHHHHHHHHHHHHc-ccchhhHHh-----------------------hhhhHHHHHhhhC----CCChhhHHHHHHHHHh
Q 040338           10 LPIARKIHAQLIST-CLISSIFLQ-----------------------LIDDDYRVFCDIG----PRYLFTYNTMINGGVR   61 (385)
Q Consensus        10 ~~~a~~~~~~~~~~-~~~~~~~~~-----------------------~~~~A~~~~~~~~----~~~~~~~~~li~~~~~   61 (385)
                      ...+..++++++.. ...|.++..                       ..++|..+|++..    +.+...|...+.....
T Consensus        32 ~~Rv~~vyerAl~~~~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~  111 (308)
T d2onda1          32 TKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHh
Confidence            34566778887765 344554433                       3467777887643    2344556666666545


Q ss_pred             hhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcc
Q 040338           62 CLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLV  141 (385)
Q Consensus        62 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~  141 (385)
                         .|+++.|..+++.+.+........+|...+..+.+.|+.+.|.++|++..+...                   .+..
T Consensus       112 ---~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~-------------------~~~~  169 (308)
T d2onda1         112 ---RMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-------------------TRHH  169 (308)
T ss_dssp             ---TTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-------------------CCTH
T ss_pred             ---cccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-------------------CcHH
Confidence               788888888888887653332344678888888888888888888888765542                   3333


Q ss_pred             hHHHHHHH-HHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC-CCchHHHHHHHHH
Q 040338          142 SWNTMISI-LTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP-SLDVFVGSGLIDM  219 (385)
Q Consensus       142 ~~~~li~~-~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~  219 (385)
                      .|...... +...|+.+.|..+|+.+.+. .+-+...+...+..+.+.|+.+.|..+|++.++... .|..         
T Consensus       170 ~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~---------  239 (308)
T d2onda1         170 VYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEK---------  239 (308)
T ss_dssp             HHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGG---------
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHH---------
Confidence            44333322 33457788888888888775 333566777778888888888888888888777543 2221         


Q ss_pred             HHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          220 YLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       220 ~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                                 ....|...+..-...|+.+.+.++++++.+
T Consensus       240 -----------~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         240 -----------SGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             -----------CHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             -----------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                       122445555555666788888888877754

>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=98.74  E-value=3.1e-07  Score=75.07  Aligned_cols=96  Identities=7%  Similarity=-0.070  Sum_probs=79.8

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLID  218 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  218 (385)
                      ..+|..+..+|.+.|++++|+..|++..+.  .| +..+|..+..++.+.|++++|+..|++.++..+            
T Consensus        37 a~~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p------------  102 (259)
T d1xnfa_          37 AQLLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP------------  102 (259)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT------------
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHh------------
Confidence            346777788899999999999999999874  55 577888899999999999999999999988753            


Q ss_pred             HHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc
Q 040338          219 MYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR  260 (385)
Q Consensus       219 ~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  260 (385)
                                 .+..++..+...|...|++++|...|+...+
T Consensus       103 -----------~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_         103 -----------TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             -----------TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----------hhhhhHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence                       2334668889999999999999999988765

>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=98.70  E-value=3.3e-07  Score=74.90  Aligned_cols=119  Identities=10%  Similarity=-0.106  Sum_probs=84.2

Q ss_pred             ChHHHHHHHHHHHHhccCC---CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchH
Q 040338           67 NIKMALHLHGLVKKFYFVS---DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSW  143 (385)
Q Consensus        67 ~~~~a~~~~~~m~~~g~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  143 (385)
                      +.+.++.-+++........   ...+|..+..+|.+.|++++|.+.|++..+.+                   +.+..+|
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-------------------p~~~~a~   74 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-------------------PDMPEVF   74 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------CCCHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-------------------CCCHHHH
Confidence            3445555555555432111   23466667778888888888888887776544                   3567788


Q ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHCCCCC-CHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          144 NTMISILTRHGFGFETLCTFIELWNHGFGL-SSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       144 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      +.+..+|.+.|++++|+..|++..+.  .| +..++..+..++...|++++|.+.++..++..+
T Consensus        75 ~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p  136 (259)
T d1xnfa_          75 NYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP  136 (259)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             hhhchHHHHHHHHHHhhhhhhHHHHH--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhcc
Confidence            88888888888888888888888774  44 355677777788888888888888888877653

>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=98.69  E-value=2.9e-07  Score=78.59  Aligned_cols=250  Identities=7%  Similarity=-0.043  Sum_probs=157.5

Q ss_pred             CChHHHHHHHHHHHHhccCCCc-hHHHhHHHH----------HHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcC
Q 040338           66 GNIKMALHLHGLVKKFYFVSDE-SIAKSSIDM----------HVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQK  134 (385)
Q Consensus        66 ~~~~~a~~~~~~m~~~g~~~~~-~~~~~li~~----------~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~  134 (385)
                      ...++|+++++...+.  .|+. ..|+..-..          +...|++++|+.+++...+.+                 
T Consensus        43 ~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-----------------  103 (334)
T d1dcea1          43 ELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-----------------  103 (334)
T ss_dssp             CCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-----------------
T ss_pred             cccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-----------------
Confidence            4458999999999986  4554 344433222          223344677777777765544                 


Q ss_pred             CCCCCcchHHHHHHHHHhCCC--chHHHHHHHHHHHCCCCCCHhhHH-HHHHHhcCccCccchhhHHHHHHHhCCCCchH
Q 040338          135 MPERDLVSWNTMISILTRHGF--GFETLCTFIELWNHGFGLSSMLYA-TAFSARASVYDLEWGPHLHSRVVHMEPSLDVF  211 (385)
Q Consensus       135 ~~~~~~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~g~~p~~~t~~-~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  211 (385)
                        +.+...|..+..++...++  +++|+..+.++.+.. +++...+. .....+...+..++|+..++.+++..+ -+..
T Consensus       104 --pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~  179 (334)
T d1dcea1         104 --PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYS  179 (334)
T ss_dssp             --TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHH
T ss_pred             --CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHH
Confidence              4567778888777777664  789999999998752 23455543 444677788999999999998887754 3444


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHH-----
Q 040338          212 VGSGLIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFF-----  286 (385)
Q Consensus       212 ~~~~li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~-----  286 (385)
                      .|+.+...+.+                      .|++++|...++...+-.... ......+...+..+++...+     
T Consensus       180 a~~~l~~~~~~----------------------~~~~~~A~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~a~~~~~~~l~  236 (334)
T d1dcea1         180 SWHYRSCLLPQ----------------------LHPQPDSGPQGRLPENVLLKE-LELVQNAFFTDPNDQSAWFYHRWLL  236 (334)
T ss_dssp             HHHHHHHHHHH----------------------HSCCCCSSSCCSSCHHHHHHH-HHHHHHHHHHCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHH----------------------hcCHHHHHHHHHHhHHhHHHH-HHHHHHHHHhcchhHHHHHHHHHHH
Confidence            45444444444                      445444443333322211111 11222334445555555444     


Q ss_pred             -------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CCCc-chHHHH
Q 040338          287 -------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KPTC-VIWGAL  355 (385)
Q Consensus       287 -------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~~-~~~~~l  355 (385)
                             .+..+...+...++.++|...+.+..+..+  ...+..+...|.+.|+.++|.+.|+...+ .|+. .-|..|
T Consensus       237 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~~~L  316 (334)
T d1dcea1         237 GRAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDL  316 (334)
T ss_dssp             SCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             hCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcccHHHHHHH
Confidence                   333444555566788888888888887777  77778888888999999999999988876 3643 355666


Q ss_pred             HHHHHh
Q 040338          356 LGACCS  361 (385)
Q Consensus       356 i~~~~~  361 (385)
                      ...+..
T Consensus       317 ~~~~~~  322 (334)
T d1dcea1         317 RSKFLL  322 (334)
T ss_dssp             HHHHHH
T ss_pred             HHHHhH
Confidence            555554

>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=98.56  E-value=5.9e-07  Score=74.98  Aligned_cols=208  Identities=13%  Similarity=0.033  Sum_probs=110.5

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHHC----CCCCCH-hhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWNH----GFGLSS-MLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGL  216 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  216 (385)
                      .|......|...+++++|.+.|.+..+.    +-+++. .+|..+..+|.+.|++++|.+.++.....            
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~------------  106 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQI------------  106 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH------------
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHH------------
Confidence            3555555555666666666666555432    111222 13444555555555555555555444332            


Q ss_pred             HHHHHhcCCCCCCchhhHHHHHHHHHHc-CCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHh
Q 040338          217 IDMYLKCGCNGIESSIQIGKALVTMYAE-GGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGC  295 (385)
Q Consensus       217 i~~~~~~g~~~~~~~~~~~~~li~~~~~-~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~  295 (385)
                         +...|+  ......++..+...|.. .|++++|++.+++..+           .+-..++..  ...-++..+...+
T Consensus       107 ---~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~-----------l~~~~~~~~--~~~~~~~~la~~~  168 (290)
T d1qqea_         107 ---FTHRGQ--FRRGANFKFELGEILENDLHDYAKAIDCYELAGE-----------WYAQDQSVA--LSNKCFIKCADLK  168 (290)
T ss_dssp             ---HHHTTC--HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-----------HHHHTTCHH--HHHHHHHHHHHHH
T ss_pred             ---hhhccc--chhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH-----------HHHhcCchh--hhhhHHHHHHHHH
Confidence               111111  11123334444444432 3555555555544321           011111100  0000567777788


Q ss_pred             cccCChhhHHHHHHHHHhccc---------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C---Cc---chHHHHHHHH
Q 040338          296 SHSGPVTKGKHYFTAMAKFTY---------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P---TC---VIWGALLGAC  359 (385)
Q Consensus       296 ~~~~~~~~a~~~~~~~~~~~~---------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p---~~---~~~~~li~~~  359 (385)
                      ...|++++|...++++.....         ...+...+..+...|+++.|.+.+++..+. |   +.   .....++.++
T Consensus       169 ~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~  248 (290)
T d1qqea_         169 ALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAV  248 (290)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHH
T ss_pred             HHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHH
Confidence            888888888888888777554         223445556677789999999999988764 2   22   2445566666


Q ss_pred             Hh--cCChHHHHHHHHHHHhcc
Q 040338          360 CS--HYNTKLAELVMRNLLQLD  379 (385)
Q Consensus       360 ~~--~g~~~~a~~~~~~~~~~~  379 (385)
                      ..  .+.+++|+.-|+++.+.+
T Consensus       249 ~~~d~e~~~eai~~y~~~~~lD  270 (290)
T d1qqea_         249 NEGDSEQLSEHCKEFDNFMRLD  270 (290)
T ss_dssp             HTTCTTTHHHHHHHHTTSSCCC
T ss_pred             HhcCHHHHHHHHHHHHHHhhcC
Confidence            55  234678887777666554

>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=98.54  E-value=1.2e-06  Score=72.95  Aligned_cols=144  Identities=13%  Similarity=0.022  Sum_probs=103.8

Q ss_pred             HHHHHHcCCChhHHHHHHHhccc-----CC----hhhHHHHHHHHHhcCCCCchHHHH------------------HHHH
Q 040338          238 LVTMYAEGGSTQKADLAFELMSR-----RN----MISWMVLISAFSQAGVLEKPRFFF------------------FFVS  290 (385)
Q Consensus       238 li~~~~~~g~~~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~------------------~~~~  290 (385)
                      ....|...|++++|.+.|.+..+     .+    ..+|..+..+|.+.|++++|++.+                  ++..
T Consensus        43 aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  122 (290)
T d1qqea_          43 AATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFE  122 (290)
T ss_dssp             HHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHH
Confidence            34566677788888887776653     11    246777777888888888887777                  5666


Q ss_pred             HHHHhc-ccCChhhHHHHHHHHHhccc--------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-CCc--------chH
Q 040338          291 LLSGCS-HSGPVTKGKHYFTAMAKFTY--------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-PTC--------VIW  352 (385)
Q Consensus       291 l~~~~~-~~~~~~~a~~~~~~~~~~~~--------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~--------~~~  352 (385)
                      +...|. ..|++++|...+++..+...        ..++..+...+.+.|++++|.+.|++.... |+.        ..|
T Consensus       123 l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~  202 (290)
T d1qqea_         123 LGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYF  202 (290)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHH
T ss_pred             HHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHH
Confidence            666664 46999999999988765322        556788899999999999999999886542 111        123


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          353 GALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       353 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ...+..+...|+++.|...+++..+..|.
T Consensus       203 ~~~~~~~l~~~d~~~A~~~~~~~~~~~~~  231 (290)
T d1qqea_         203 LKKGLCQLAATDAVAAARTLQEGQSEDPN  231 (290)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHGGGCC---
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            44555677889999999999999887664

>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=98.37  E-value=5.2e-06  Score=64.34  Aligned_cols=124  Identities=14%  Similarity=-0.066  Sum_probs=66.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|+++.|++.|.++    .+|+..+|..+..+|...|++++|++.|++..+.+                   +.+...|.
T Consensus        18 ~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-------------------p~~~~a~~   74 (192)
T d1hh8a_          18 KKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-------------------KHLAVAYF   74 (192)
T ss_dssp             TTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             CCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-------------------hhhhhhHH
Confidence            46666666655543    23455555556666666666666666665554433                   24455555


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCC------------C--CCC-HhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCc
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHG------------F--GLS-SMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLD  209 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g------------~--~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  209 (385)
                      .+..+|.+.|++++|++.|++.....            .  .++ ..++..+..++.+.|++++|.+.++...+..+.+.
T Consensus        75 ~~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~  154 (192)
T d1hh8a_          75 QRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPR  154 (192)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGG
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcc
Confidence            56666666666666666665554320            0  000 12333444556666666666666666655544443


Q ss_pred             hH
Q 040338          210 VF  211 (385)
Q Consensus       210 ~~  211 (385)
                      ..
T Consensus       155 ~~  156 (192)
T d1hh8a_         155 HS  156 (192)
T ss_dssp             GG
T ss_pred             hH
Confidence            33

>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=98.29  E-value=1.9e-05  Score=61.03  Aligned_cols=143  Identities=6%  Similarity=-0.241  Sum_probs=101.6

Q ss_pred             hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHh
Q 040338           33 LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLR  112 (385)
Q Consensus        33 ~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  112 (385)
                      +++.|.+.|+++..|+...|..+-..+..   .|++++|++.|++.++.. +-+...|..+..+|.+.|+.++|++.|++
T Consensus        20 d~~~Al~~~~~i~~~~~~~~~nlG~~~~~---~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~~~~~k   95 (192)
T d1hh8a_          20 DWKGALDAFSAVQDPHSRICFNIGCMYTI---LKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKE   95 (192)
T ss_dssp             CHHHHHHHHHTSSSCCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHhcCCCCHHHHHHHHHHHHH---cCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHHHHHHH
Confidence            89999999999999999888888888766   999999999999999976 34678899999999999999999999987


Q ss_pred             ccCCCccccccchHHHHHHhcCCCCC-CcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040338          113 MLNPSLFCWKFGIIRLLIMFQKMPER-DLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFS  183 (385)
Q Consensus       113 m~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  183 (385)
                      .........  .++  ...+....++ ...++..+..++.+.|++++|.+.|....+....|........+.
T Consensus        96 Al~~~~~n~--~~~--~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~~~~~~Al~  163 (192)
T d1hh8a_          96 ALIQLRGNQ--LID--YKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAME  163 (192)
T ss_dssp             HHHTTTTCS--EEE--CGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHHHHHHH
T ss_pred             HHHhCccCc--hHH--HHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcchHHHHHHHH
Confidence            532110000  000  0000000001 123455677789999999999999999887655554444433333

>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=98.29  E-value=1.7e-06  Score=61.20  Aligned_cols=93  Identities=8%  Similarity=-0.110  Sum_probs=82.2

Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChH
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTK  366 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~  366 (385)
                      -...+...|++++|+..|++..+..+  ...|..+..+|.+.|++++|++.++.....  .+...|..+..++...|+++
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHH
Confidence            34567788999999999999998888  888999999999999999999999988762  46778999999999999999


Q ss_pred             HHHHHHHHHHhccccCC
Q 040338          367 LAELVMRNLLQLDVKVF  383 (385)
Q Consensus       367 ~a~~~~~~~~~~~~~~~  383 (385)
                      +|+..+++.++..|.++
T Consensus        89 ~A~~~~~~a~~~~p~~~  105 (117)
T d1elwa_          89 EAKRTYEEGLKHEANNP  105 (117)
T ss_dssp             HHHHHHHHHHTTCTTCH
T ss_pred             HHHHHHHHHHHhCCCCH
Confidence            99999999999888764

>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=98.21  E-value=0.00017  Score=60.30  Aligned_cols=45  Identities=7%  Similarity=0.003  Sum_probs=26.1

Q ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCc
Q 040338          143 WNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASV  188 (385)
Q Consensus       143 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  188 (385)
                      -..++..|-..|.+++...+++..... -.++...++.++..|++.
T Consensus       102 l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~  146 (336)
T d1b89a_         102 LEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKF  146 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHh
Confidence            345666666667777766666655422 233455556666666653

>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=98.19  E-value=2.6e-06  Score=60.49  Aligned_cols=95  Identities=14%  Similarity=-0.070  Sum_probs=80.5

Q ss_pred             HHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCH---HHHHHHHHhCCCC-CCc---chHHHHHHHH
Q 040338          289 VSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLL---GEAKKLIDEMPSK-PTC---VIWGALLGAC  359 (385)
Q Consensus       289 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~---~~A~~~~~~m~~~-p~~---~~~~~li~~~  359 (385)
                      ..+++.+...+++++|.+.|++....++  +.++..+..++.+.++.   ++|+++|++.... |+.   .+|..+..+|
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            4577888889999999999999999888  78888889999876655   4699999998764 332   3678899999


Q ss_pred             HhcCChHHHHHHHHHHHhccccCC
Q 040338          360 CSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       360 ~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      .+.|++++|++.|+++++.+|.+.
T Consensus        83 ~~~g~~~~A~~~~~~aL~~~P~~~  106 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQTEPQNN  106 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHhhhHHHHHHHHHHHHhCcCCH
Confidence            999999999999999999988754

>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=98.16  E-value=5.4e-06  Score=64.57  Aligned_cols=93  Identities=5%  Similarity=-0.200  Sum_probs=79.1

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCCh
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNT  365 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~  365 (385)
                      .....+.+.|++++|+..|++.....+  +..|..+..+|.+.|++++|+..|+...+- | +..+|..+..+|...|++
T Consensus         9 ~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~~~   88 (201)
T d2c2la1           9 EQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESY   88 (201)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCCCH
Confidence            345667788899999999999888877  888888999999999999999999998873 5 466888999999999999


Q ss_pred             HHHHHHHHHHHhccccC
Q 040338          366 KLAELVMRNLLQLDVKV  382 (385)
Q Consensus       366 ~~a~~~~~~~~~~~~~~  382 (385)
                      ++|+..|++..+..|.+
T Consensus        89 ~~A~~~~~~al~l~p~~  105 (201)
T d2c2la1          89 DEAIANLQRAYSLAKEQ  105 (201)
T ss_dssp             HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCccc
Confidence            99999999988877653

>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=98.13  E-value=4.4e-06  Score=62.58  Aligned_cols=76  Identities=8%  Similarity=-0.056  Sum_probs=45.7

Q ss_pred             HHHHHhcCCCCchHHHH------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHH
Q 040338          270 ISAFSQAGVLEKPRFFF------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGE  335 (385)
Q Consensus       270 i~~~~~~g~~~~a~~~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~  335 (385)
                      ...|.+.|++++|+..|            .|..+..+|...|++++|.+.|+++.+..+  ...+..+..++...|++++
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~~~e   96 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRA   96 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCCHHH
Confidence            44455666666666666            555666666666666666666666655555  5555556666666666666


Q ss_pred             HHHHHHhCCC
Q 040338          336 AKKLIDEMPS  345 (385)
Q Consensus       336 A~~~~~~m~~  345 (385)
                      |.+.+++...
T Consensus        97 A~~~~~~a~~  106 (159)
T d1a17a_          97 ALRDYETVVK  106 (159)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            6666655544

>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=98.12  E-value=1.9e-05  Score=55.55  Aligned_cols=89  Identities=17%  Similarity=0.012  Sum_probs=70.0

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|+..|++..+.. +-+...|..+..+|.+.|++++|+..+++..+.+                   +.+...|.
T Consensus        16 ~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~~~~   75 (117)
T d1elwa_          16 VGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-------------------PDWGKGYS   75 (117)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-------------------cchhhHHH
Confidence            788888888888888764 3467778888888888888888888888776655                   46777888


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCH
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSS  175 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  175 (385)
                      .+..++...|++++|+..|++..+.  .|+.
T Consensus        76 ~~g~~~~~~~~~~~A~~~~~~a~~~--~p~~  104 (117)
T d1elwa_          76 RKAAALEFLNRFEEAKRTYEEGLKH--EANN  104 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTT--CTTC
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHh--CCCC
Confidence            8888888888888888888888763  5543

>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=98.05  E-value=4e-05  Score=59.35  Aligned_cols=98  Identities=8%  Similarity=-0.158  Sum_probs=80.8

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHH
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIR  127 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  127 (385)
                      +....-..-..+..   .|++++|+..|++..+.. +.+...|..+..+|.+.|++++|+..|++..+.+          
T Consensus         3 ~a~~l~~~Gn~~~~---~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~----------   68 (201)
T d2c2la1           3 SAQELKEQGNRLFV---GRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD----------   68 (201)
T ss_dssp             CHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC----------
T ss_pred             hHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC----------
Confidence            33333333344444   899999999999999875 4578889999999999999999999999987765          


Q ss_pred             HHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          128 LLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       128 a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                               +-+..+|..+..+|.+.|++++|+..|++..+
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                     35677899999999999999999999998865

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.02  E-value=0.00069  Score=54.69  Aligned_cols=219  Identities=11%  Similarity=-0.102  Sum_probs=132.6

Q ss_pred             cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcC----ccCccchhhHHHHHHHhCCCCchHHHHH
Q 040338          140 LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARAS----VYDLEWGPHLHSRVVHMEPSLDVFVGSG  215 (385)
Q Consensus       140 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  215 (385)
                      +..+..|-..+.+.+++++|+++|++..+.|   +...+..|-..|..    ..+...+...+....+.+..   .....
T Consensus         2 p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~---~a~~~   75 (265)
T d1ouva_           2 PKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYS---NGCHL   75 (265)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH---HHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccccc---chhhc
Confidence            4456667777788999999999999998876   34444445444443    45666777777776665531   22222


Q ss_pred             HHHHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhcccC-ChhhHHHHHHHHHhcCCCC----chHHHH----
Q 040338          216 LIDMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSRR-NMISWMVLISAFSQAGVLE----KPRFFF----  286 (385)
Q Consensus       216 li~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~li~~~~~~g~~~----~a~~~~----  286 (385)
                      +...+....                  ...++.+.|...++...+. .......+...+.......    .+...+    
T Consensus        76 l~~~~~~~~------------------~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~  137 (265)
T d1ouva_          76 LGNLYYSGQ------------------GVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKAC  137 (265)
T ss_dssp             HHHHHHHTS------------------SSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHH
T ss_pred             ccccccccc------------------ccchhhHHHHHHHhhhhhhhhhhHHHhhcccccCCCcccchhHHHHHHhhhhh
Confidence            222221111                  1123455566655554432 2223333333333222111    111222    


Q ss_pred             ------HHHHHHHHhc----ccCChhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCCCCcchH
Q 040338          287 ------FFVSLLSGCS----HSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSKPTCVIW  352 (385)
Q Consensus       287 ------~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~  352 (385)
                            .+..+...+.    ...+...+...++...+.+.......+...|..    ..++++|...|+...+.-+...+
T Consensus       138 ~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g~~~a~  217 (265)
T d1ouva_         138 DLNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGC  217 (265)
T ss_dssp             HTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cccccchhhhhhhhhccCCCcccccccchhhhhccccccccccccchhhhcccCcccccchhhhhhhHhhhhcccCHHHH
Confidence                  3444444444    356677888888888887775555556666654    66899999999988776667777


Q ss_pred             HHHHHHHHh----cCChHHHHHHHHHHHhccccC
Q 040338          353 GALLGACCS----HYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       353 ~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ..|...|..    ..+.++|.++|++..+.|..+
T Consensus       218 ~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         218 FNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             HHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHcCCCCccCHHHHHHHHHHHHHCcCHH
Confidence            778888775    448899999999998887654

>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=98.00  E-value=0.00053  Score=57.23  Aligned_cols=282  Identities=8%  Similarity=-0.021  Sum_probs=157.6

Q ss_pred             ccccCCChHHHHHHHHHHHHcccchhhHHh--hhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHH
Q 040338            3 ACGSLKSLPIARKIHAQLISTCLISSIFLQ--LIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKK   80 (385)
Q Consensus         3 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~   80 (385)
                      -|-+.|.++.|..++..+..-.-.....+.  +++.|..++.+..  +..+|..+...+..   ......+     .+..
T Consensus        23 ~c~~~~lye~A~~lY~~~~d~~rl~~~~v~l~~~~~avd~~~k~~--~~~~~k~~~~~l~~---~~e~~la-----~i~~   92 (336)
T d1b89a_          23 RCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVD---GKEFRLA-----QMCG   92 (336)
T ss_dssp             ------CTTTHHHHHHHTTCHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHH---TTCHHHH-----HHTT
T ss_pred             HHHHCCCHHHHHHHHHhCCCHHHHHHHHHhhccHHHHHHHHHHcC--CHHHHHHHHHHHHh---CcHHHHH-----HHHH
Confidence            466778888888888755443222222222  6777777777644  55678878777554   4444332     2223


Q ss_pred             hccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHH
Q 040338           81 FYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETL  160 (385)
Q Consensus        81 ~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~  160 (385)
                      .+...++.....++..|-..|..++...+++......                   .++...++-++..|++.+ +++..
T Consensus        93 ~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-------------------~~~~~~~~~L~~lyak~~-~~kl~  152 (336)
T d1b89a_          93 LHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-------------------RAHMGMFTELAILYSKFK-PQKMR  152 (336)
T ss_dssp             TTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-------------------TCCHHHHHHHHHHHHTTC-HHHHH
T ss_pred             HHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-------------------ccchHHHHHHHHHHHHhC-hHHHH
Confidence            3344566667789999999999999999998765443                   467778899999999875 44444


Q ss_pred             HHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHH
Q 040338          161 CTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVT  240 (385)
Q Consensus       161 ~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~  240 (385)
                      +.+...   +..   .-...+++.|-+.+-++++.-++..+...    +..+ ..++.         ..++..-....+.
T Consensus       153 e~l~~~---s~~---y~~~k~~~~c~~~~l~~elv~Ly~~~~~~----~~A~-~~~i~---------~~~~~~~~~~f~e  212 (336)
T d1b89a_         153 EHLELF---WSR---VNIPKVLRAAEQAHLWAELVFLYDKYEEY----DNAI-ITMMN---------HPTDAWKEGQFKD  212 (336)
T ss_dssp             HHHHHH---STT---SCHHHHHHHHHTTTCHHHHHHHHHHTTCH----HHHH-HHHHH---------STTTTCCHHHHHH
T ss_pred             HHHHhc---ccc---CCHHHHHHHHHHcCChHHHHHHHHhcCCH----HHHH-HHHHH---------cchhhhhHHHHHH
Confidence            444332   111   22234566666666666655555443211    1000 00000         1111212233344


Q ss_pred             HHHcCCChhHHHHHHHhcccCChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccchhhH
Q 040338          241 MYAEGGSTQKADLAFELMSRRNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTYTCYF  320 (385)
Q Consensus       241 ~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  320 (385)
                      .+.+..+.+...++.....+.++...+.++......-++.+         ++.-..+.+++......++.....+...+.
T Consensus       213 ~~~k~~N~e~~~~~i~~yL~~~p~~i~~lL~~v~~~~d~~r---------~V~~~~k~~~l~li~p~Le~v~~~n~~~vn  283 (336)
T d1b89a_         213 IITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTR---------AVNYFSKVKQLPLVKPYLRSVQNHNNKSVN  283 (336)
T ss_dssp             HHHHCSSTHHHHHHHHHHHHHCGGGHHHHHHHHGGGCCHHH---------HHHHHHHTTCTTTTHHHHHHHHTTCCHHHH
T ss_pred             HHHccCChHHHHHHHHHHHHcCHHHHHHHHHHhccCCCHHH---------HHHHHHhcCCcHHHHHHHHHHHHcChHHHH
Confidence            45555555544444433333233333444444444444333         334446677777777888777776666788


Q ss_pred             HHHHHHHHccCCHHHHHHHHHhC
Q 040338          321 VCMVDLLGLSGLLGEAKKLIDEM  343 (385)
Q Consensus       321 ~~li~~~~~~g~~~~A~~~~~~m  343 (385)
                      +++.+.|...++++.-.+..+.-
T Consensus       284 ~al~~lyie~~d~~~l~~~i~~~  306 (336)
T d1b89a_         284 ESLNNLFITEEDYQALRTSIDAY  306 (336)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHC
T ss_pred             HHHHHHHhCcchhHHHHHHHHHh
Confidence            88888888888877666665443

>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=97.97  E-value=1.2e-05  Score=56.04  Aligned_cols=86  Identities=13%  Similarity=-0.004  Sum_probs=75.5

Q ss_pred             HHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChH
Q 040338          291 LLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTK  366 (385)
Q Consensus       291 l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~  366 (385)
                      +...+.+.|++++|...|++..+..+  ...+..+..++.+.|++++|+..|+...+ .| +...|..+...|...|+++
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~~  101 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNAN  101 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCCCHH
Confidence            34556778999999999999999888  88999999999999999999999998876 34 5678999999999999999


Q ss_pred             HHHHHHHHHH
Q 040338          367 LAELVMRNLL  376 (385)
Q Consensus       367 ~a~~~~~~~~  376 (385)
                      +|.+.+++.+
T Consensus       102 ~A~~~l~~~l  111 (112)
T d1hxia_         102 AALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999999864

>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=97.95  E-value=2.5e-05  Score=55.23  Aligned_cols=99  Identities=10%  Similarity=-0.153  Sum_probs=72.4

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC---hhHHHHHHHhccCCCccccccchHHHHH
Q 040338           54 TMINGGVRCLCVGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA---VDYAESAFLRMLNPSLFCWKFGIIRLLI  130 (385)
Q Consensus        54 ~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~~~~~~~~~~~~a~~  130 (385)
                      .+++.+..   .+++++|.+.|+...+.+ +.++.++..+..++.+.++   .++|+++|++....+.            
T Consensus         4 ~l~n~~~~---~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~------------   67 (122)
T d1nzna_           4 AVLNELVS---VEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGS------------   67 (122)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSC------------
T ss_pred             HHHHHhcC---HHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccC------------
Confidence            45555555   788899999999888875 4477888888888877554   4568888888776553            


Q ss_pred             HhcCCCCCC-cchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHh
Q 040338          131 MFQKMPERD-LVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSM  176 (385)
Q Consensus       131 ~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  176 (385)
                            .|+ ..+|..|..+|.+.|++++|.+.|++..+.  .|+..
T Consensus        68 ------~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~~--~P~~~  106 (122)
T d1nzna_          68 ------KEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQNN  106 (122)
T ss_dssp             ------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             ------CchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--CcCCH
Confidence                  233 346777888888899999999999988874  56543

>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=97.94  E-value=3.2e-05  Score=57.69  Aligned_cols=85  Identities=8%  Similarity=-0.004  Sum_probs=75.4

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|+..|++..+.. +-+...|..+..+|...|++++|...|++..+.+                   +.+..+|.
T Consensus        23 ~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-------------------p~~~~a~~   82 (159)
T d1a17a_          23 AKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-------------------KKYIKGYY   82 (159)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             cCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-------------------ccchHHHH
Confidence            899999999999999975 4477889999999999999999999999887655                   46778899


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      .+..++...|++++|...+++....
T Consensus        83 ~~g~~~~~~g~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          83 RRAASNMALGKFRAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            9999999999999999999999885

>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=97.82  E-value=4.4e-05  Score=53.05  Aligned_cols=83  Identities=12%  Similarity=-0.061  Sum_probs=73.3

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|...|++..+... -+...|..+..++.+.|++++|+..|++..+.+                   +.+..+|.
T Consensus        29 ~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-------------------p~~~~a~~   88 (112)
T d1hxia_          29 LANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-------------------PKDIAVHA   88 (112)
T ss_dssp             TTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHH
T ss_pred             HhhhHHHHHHHhhhccccc-ccchhhhhhhhhhhhhhhHHHhhcccccccccc-------------------cccccchH
Confidence            7999999999999998753 378899999999999999999999999877655                   46788999


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHH
Q 040338          145 TMISILTRHGFGFETLCTFIELW  167 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~  167 (385)
                      .+..+|...|++++|++.|++..
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=97.75  E-value=0.00014  Score=55.13  Aligned_cols=34  Identities=15%  Similarity=0.080  Sum_probs=22.7

Q ss_pred             ChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHh
Q 040338           48 YLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKF   81 (385)
Q Consensus        48 ~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~   81 (385)
                      |...|..+...-......|++++|.+.|....+.
T Consensus         7 D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l   40 (179)
T d2ff4a2           7 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALRE   40 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence            3444555555444445578999998888888774

>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=97.74  E-value=6.6e-05  Score=56.57  Aligned_cols=79  Identities=4%  Similarity=-0.107  Sum_probs=44.0

Q ss_pred             HHHHHHHHhcCCCCchHHHH---------------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc--h
Q 040338          267 MVLISAFSQAGVLEKPRFFF---------------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T  317 (385)
Q Consensus       267 ~~li~~~~~~g~~~~a~~~~---------------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~  317 (385)
                      ......+.+.|++++|+..|                           +|+.+..+|.+.|++++|...++...+..+  +
T Consensus        17 ~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~   96 (170)
T d1p5qa1          17 KERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNE   96 (170)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhccccch
Confidence            34455666777777777666                           344445555555555555555555555444  4


Q ss_pred             hhHHHHHHHHHccCCHHHHHHHHHhCCC
Q 040338          318 CYFVCMVDLLGLSGLLGEAKKLIDEMPS  345 (385)
Q Consensus       318 ~~~~~li~~~~~~g~~~~A~~~~~~m~~  345 (385)
                      ..+..+..+|...|++++|...|+...+
T Consensus        97 ~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          97 KGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4455555555555555555555555543

>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=97.68  E-value=4.2e-05  Score=54.63  Aligned_cols=94  Identities=7%  Similarity=-0.018  Sum_probs=76.5

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC----CC-----cchHHHHH
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK----PT-----CVIWGALL  356 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----p~-----~~~~~~li  356 (385)
                      +-.+...+...|++++|+..|++..+.++  ...+..+..+|.+.|++++|++.++++.+-    +.     ..+|..+.
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            34566778888999999999999998888  888888999999999999999999887652    22     24677788


Q ss_pred             HHHHhcCChHHHHHHHHHHHhcccc
Q 040338          357 GACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       357 ~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      ..+...+++++|+..+++.....+.
T Consensus        87 ~~~~~~~~~~~A~~~~~kal~~~~~  111 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYNKSLAEHRT  111 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcCCC
Confidence            8888899999999999988765543

>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=97.58  E-value=0.00019  Score=52.89  Aligned_cols=67  Identities=7%  Similarity=-0.145  Sum_probs=57.8

Q ss_pred             hhhHHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          317 TCYFVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       317 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ..++.-+..+|.+.|++++|++.++...+ .| +..+|..+..+|...|++++|+..|++.++.+|.+.
T Consensus        67 ~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~  135 (153)
T d2fbna1          67 ISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNL  135 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCH
T ss_pred             HHHHhhHHHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCH
Confidence            45666788889999999999999998876 34 678999999999999999999999999999988754

>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=97.49  E-value=0.00034  Score=52.43  Aligned_cols=67  Identities=4%  Similarity=-0.253  Sum_probs=55.7

Q ss_pred             hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccCC
Q 040338          317 TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKVF  383 (385)
Q Consensus       317 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  383 (385)
                      ...+..+..++.+.|++++|+..++...+.  .+...|..+..+|...|++++|+..|++.++.+|.+.
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~  145 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDK  145 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCH
Confidence            455666788889999999999999888763  4566888899999999999999999999998887653

>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=97.43  E-value=0.00011  Score=52.33  Aligned_cols=99  Identities=9%  Similarity=-0.065  Sum_probs=78.3

Q ss_pred             HHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338           90 AKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus        90 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                      +..+...|.+.|++++|+..|.+..+.+                   +.+..+|..+..+|.+.|++++|+..++++.+.
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~-------------------p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l   67 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD-------------------PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEV   67 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHh
Confidence            4566778899999999999998887655                   467889999999999999999999999998763


Q ss_pred             CCC-CC-----HhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          170 GFG-LS-----SMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       170 g~~-p~-----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                      ... +.     ..+|..+-..+...+++++|++.|+........
T Consensus        68 ~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~~~~  111 (128)
T d1elra_          68 GRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRT  111 (128)
T ss_dssp             HHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC
Confidence            210 11     235666777788888999999999988776433

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.42  E-value=0.0087  Score=47.85  Aligned_cols=216  Identities=7%  Similarity=-0.064  Sum_probs=118.3

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHHHHHHHHHh----CCCchHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWNTMISILTR----HGFGFETLC  161 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~  161 (385)
                      |+..+..|-..+-+.++.++|++.|++..+.|                     |...+-.|-..|..    ..++..|..
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---------------------~~~A~~~Lg~~y~~G~~~~~d~~~a~~   59 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---------------------ENSGCFNLGVLYYQGQGVEKNLKKAAS   59 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---------------------CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---------------------CHHHHHHHHHHHHcCCCcchhHHHHHH
Confidence            34556667777778899999999998875533                     33444445555554    557788888


Q ss_pred             HHHHHHHCCCCCCHhhHHH-HHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHHHHHHhcCCCCCCchhhHHHHHHH
Q 040338          162 TFIELWNHGFGLSSMLYAT-AFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLIDMYLKCGCNGIESSIQIGKALVT  240 (385)
Q Consensus       162 ~~~~m~~~g~~p~~~t~~~-ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~~~~~~~~~~li~  240 (385)
                      ++....+.+.+.-...... .........+.+.|...++.....|....   ...+...+....                
T Consensus        60 ~~~~a~~~~~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a---~~~l~~~~~~~~----------------  120 (265)
T d1ouva_          60 FYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEG---CASLGGIYHDGK----------------  120 (265)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH---HHHHHHHHHHCS----------------
T ss_pred             hhcccccccccchhhccccccccccccchhhHHHHHHHhhhhhhhhhhH---HHhhcccccCCC----------------
Confidence            8888777653221111111 11222334566677777777776654211   111111111111                


Q ss_pred             HHHcCCChhHHHHHHHhccc-CChhhHHHHHHHHHhcCCCCchH----HHH----------HHHHHHHHhc----ccCCh
Q 040338          241 MYAEGGSTQKADLAFELMSR-RNMISWMVLISAFSQAGVLEKPR----FFF----------FFVSLLSGCS----HSGPV  301 (385)
Q Consensus       241 ~~~~~g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~~g~~~~a~----~~~----------~~~~l~~~~~----~~~~~  301 (385)
                        ........+...+....+ .+...+..|...|..........    ..+          +...+...|.    ...+.
T Consensus       121 --~~~~~~~~a~~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~  198 (265)
T d1ouva_         121 --VVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNF  198 (265)
T ss_dssp             --SSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCH
T ss_pred             --cccchhHHHHHHhhhhhcccccchhhhhhhhhccCCCcccccccchhhhhccccccccccccchhhhcccCcccccch
Confidence              112233444444444333 34445555555555432222221    111          2222322232    25689


Q ss_pred             hhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhC
Q 040338          302 TKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEM  343 (385)
Q Consensus       302 ~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m  343 (385)
                      ++|...|++..+.|.+..+..|...|.+    ..+.++|.+.|+..
T Consensus       199 ~~A~~~~~~aa~~g~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kA  244 (265)
T d1ouva_         199 KEALARYSKACELENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKG  244 (265)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHH
T ss_pred             hhhhhhHhhhhcccCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHH
Confidence            9999999999998887777777777765    33677788877654

>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=97.40  E-value=0.00033  Score=52.55  Aligned_cols=62  Identities=11%  Similarity=-0.080  Sum_probs=31.8

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhCCC-CC-CcchHHHHHHHHHhcCChHHHHHHHHHHHhcccc
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEMPS-KP-TCVIWGALLGACCSHYNTKLAELVMRNLLQLDVK  381 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  381 (385)
                      |+-+..+|.+.|++++|+..++.... .| +...|..+..+|...|++++|...|++.++.+|.
T Consensus        65 ~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~  128 (170)
T d1p5qa1          65 HLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN  128 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCC
Confidence            33344455555555555555554443 23 3444555555555555555555555555555543

>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=97.40  E-value=0.00034  Score=52.90  Aligned_cols=67  Identities=12%  Similarity=0.061  Sum_probs=53.3

Q ss_pred             hhhHHHHHHHHHccCCHHHHHHHHHhCCCC-C-CcchHHHHHHHHHhcCChHHHHHHHHHHH-----hccccCC
Q 040338          317 TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK-P-TCVIWGALLGACCSHYNTKLAELVMRNLL-----QLDVKVF  383 (385)
Q Consensus       317 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~-----~~~~~~~  383 (385)
                      ...+..+...+.+.|++++|+..++.+... | +...|..++.+|.+.|+..+|++.|+++.     ++|+.|+
T Consensus        67 ~~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~  140 (179)
T d2ff4a2          67 VLAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPG  140 (179)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcC
Confidence            345667888888899999999999888763 4 66788899999999999999999988874     3566664

>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=97.40  E-value=0.00047  Score=51.53  Aligned_cols=80  Identities=10%  Similarity=-0.052  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHhcCCCCchHHHH---------------------------HHHHHHHHhcccCChhhHHHHHHHHHhccc-
Q 040338          265 SWMVLISAFSQAGVLEKPRFFF---------------------------FFVSLLSGCSHSGPVTKGKHYFTAMAKFTY-  316 (385)
Q Consensus       265 ~~~~li~~~~~~g~~~~a~~~~---------------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-  316 (385)
                      .+......+.+.|++.+|+..|                           .|..+..+|.+.|++++|+..++...+..+ 
T Consensus        17 ~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~   96 (168)
T d1kt1a1          17 IVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA   96 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcccc
Confidence            3444556677777777777766                           233344444445555555555554444444 


Q ss_pred             -hhhHHHHHHHHHccCCHHHHHHHHHhCC
Q 040338          317 -TCYFVCMVDLLGLSGLLGEAKKLIDEMP  344 (385)
Q Consensus       317 -~~~~~~li~~~~~~g~~~~A~~~~~~m~  344 (385)
                       ...+..+..+|...|++++|.+.|++..
T Consensus        97 ~~~a~~~~~~~~~~l~~~~~A~~~~~~al  125 (168)
T d1kt1a1          97 NEKGLYRRGEAQLLMNEFESAKGDFEKVL  125 (168)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             4444444444455555555555544443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.28  E-value=0.0013  Score=58.51  Aligned_cols=146  Identities=10%  Similarity=-0.102  Sum_probs=75.8

Q ss_pred             CCcchHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          138 RDLVSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       138 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      ++...+..+...+.+.|+.++|...+......  .| ..++..+...+...|++++|...|++..+..+           
T Consensus       118 ~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P-----------  183 (497)
T d1ya0a1         118 PCRVKSSQLGIISNKQTHTSAIVKPQSSSCSY--IC-QHCLVHLGDIARYRNQTSQAESYYRHAAQLVP-----------  183 (497)
T ss_dssp             -------------------------CCHHHHH--HH-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-----------
T ss_pred             hhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC--CH-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCC-----------
Confidence            45566777777788888888888777665432  11 34566677778888888899888888887753           


Q ss_pred             HHHHhcCCCCCCchhhHHHHHHHHHHcCCChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchH------HHH--
Q 040338          218 DMYLKCGCNGIESSIQIGKALVTMYAEGGSTQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPR------FFF--  286 (385)
Q Consensus       218 ~~~~~~g~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~------~~~--  286 (385)
                                  .+...|+.|...+...|+..+|...|.+-..   |...++..|...+.+..+..++.      ..+  
T Consensus       184 ------------~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~~~~~~~~~~~~~~~~~~~  251 (497)
T d1ya0a1         184 ------------SNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDEVKTKWGVSDFIK  251 (497)
T ss_dssp             ------------TBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHHTTSCCCCCSSCCHHHHHH
T ss_pred             ------------CchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhhhhhccccccchHHH
Confidence                        2334567777788888888888888876654   56677788887777655433322      111  


Q ss_pred             HHHHHHHHhcccCChhhHHHHHH
Q 040338          287 FFVSLLSGCSHSGPVTKGKHYFT  309 (385)
Q Consensus       287 ~~~~l~~~~~~~~~~~~a~~~~~  309 (385)
                      .+..+...+....+.+....+.+
T Consensus       252 ~f~~~~~~l~~~~~~~~~~~~~~  274 (497)
T d1ya0a1         252 AFIKFHGHVYLSKSLEKLSPLRE  274 (497)
T ss_dssp             HHHHHHHHHHHTCCGGGHHHHHH
T ss_pred             HHHHHHHHHHhCCchhhHHHHHH
Confidence            33444444444455554444443

>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=97.19  E-value=0.00037  Score=50.70  Aligned_cols=114  Identities=10%  Similarity=-0.088  Sum_probs=81.7

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCC----------hhHHHHHHHhccCCCccccccchHHHHHHhcC
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGA----------VDYAESAFLRMLNPSLFCWKFGIIRLLIMFQK  134 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~  134 (385)
                      .+.+++|.+.++...+.. |.+..++..+..+|...++          +++|+..|++..+.+                 
T Consensus        10 ~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-----------------   71 (145)
T d1zu2a1          10 ILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-----------------   71 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-----------------
T ss_pred             HccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-----------------
Confidence            577899999999999875 4477788888888775443          456666666655444                 


Q ss_pred             CCCCCcchHHHHHHHHHhCC-----------CchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHH
Q 040338          135 MPERDLVSWNTMISILTRHG-----------FGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVH  203 (385)
Q Consensus       135 ~~~~~~~~~~~li~~~~~~~-----------~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~  203 (385)
                        +.+..+|+.+..+|...|           .+++|.+.|++..+  +.|+..+|..-+..+      ..+.+++.+..+
T Consensus        72 --P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~------~ka~~~~~e~~k  141 (145)
T d1zu2a1          72 --PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMT------AKAPQLHAEAYK  141 (145)
T ss_dssp             --TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH------HTHHHHHHHHHH
T ss_pred             --chhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHH------HHHHHHHHHHHH
Confidence              456778888888887654           35788888888877  578777776665544      466677777776


Q ss_pred             hCC
Q 040338          204 MEP  206 (385)
Q Consensus       204 ~~~  206 (385)
                      .|+
T Consensus       142 ~~~  144 (145)
T d1zu2a1         142 QGL  144 (145)
T ss_dssp             SSS
T ss_pred             Hhc
Confidence            654

>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=97.17  E-value=0.0012  Score=49.15  Aligned_cols=93  Identities=8%  Similarity=-0.119  Sum_probs=49.0

Q ss_pred             HHHHHhcccCChhhHHHHHHHHHhccc-----------------hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcc
Q 040338          290 SLLSGCSHSGPVTKGKHYFTAMAKFTY-----------------TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCV  350 (385)
Q Consensus       290 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~  350 (385)
                      .....+.+.|++++|...|++....-.                 ..+|.-+..+|.+.|++++|+..++.....  .+..
T Consensus        20 e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~   99 (168)
T d1kt1a1          20 EKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEK   99 (168)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcccchHH
Confidence            334445555666666666555443111                 223333445555566666666666555441  2444


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          351 IWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       351 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      +|..+..+|...|++++|...|+++++.+|.+
T Consensus       100 a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n  131 (168)
T d1kt1a1         100 GLYRRGEAQLLMNEFESAKGDFEKVLEVNPQN  131 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence            55555566666666666666666666555543

>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=97.16  E-value=0.0032  Score=45.94  Aligned_cols=64  Identities=5%  Similarity=-0.190  Sum_probs=39.4

Q ss_pred             chHHHHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhC
Q 040338          141 VSWNTMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHME  205 (385)
Q Consensus       141 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  205 (385)
                      .+|+.+..+|.+.|++++|++.++...+.. +.+..+|..+..++...|++++|...|+..++..
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~  131 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN  131 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            345556666666666666666666665541 2255666666666666666666666666666654

>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=97.14  E-value=0.0021  Score=47.88  Aligned_cols=86  Identities=12%  Similarity=-0.062  Sum_probs=51.5

Q ss_pred             cCChHHHHHHHHHHHHhc--------------c-CCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHH
Q 040338           65 VGNIKMALHLHGLVKKFY--------------F-VSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLL  129 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g--------------~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~  129 (385)
                      .|++++|++.|.+..+..              . +.....|..+..+|.+.|++++|+..+++..+.+            
T Consensus        40 ~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~------------  107 (169)
T d1ihga1          40 SQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID------------  107 (169)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC------------
T ss_pred             cCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh------------
Confidence            688888888887765420              0 1123344555556666666666666666655544            


Q ss_pred             HHhcCCCCCCcchHHHHHHHHHhCCCchHHHHHHHHHHHC
Q 040338          130 IMFQKMPERDLVSWNTMISILTRHGFGFETLCTFIELWNH  169 (385)
Q Consensus       130 ~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  169 (385)
                             +.+..+|..+..++.+.|++++|+..|++..+.
T Consensus       108 -------p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1         108 -------PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             -------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -------hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence                   345556666666666666666666666666653

>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=97.09  E-value=9.6e-05  Score=59.89  Aligned_cols=122  Identities=14%  Similarity=0.039  Sum_probs=76.8

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|++++|+..+++.++.. +-|...+..+...|+..|++++|.+.|+...+.++                   .+...+.
T Consensus         9 ~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P-------------------~~~~~~~   68 (264)
T d1zbpa1           9 EGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFP-------------------EYLPGAS   68 (264)
T ss_dssp             TTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCG-------------------GGHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-------------------CcHHHHH
Confidence            699999999999999875 44778899999999999999999999988765442                   2334444


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  206 (385)
                      .+...+...+..+++..-...-...+-+++...+......+...|+.++|.+.++.+.+...
T Consensus        69 ~l~~ll~a~~~~~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p  130 (264)
T d1zbpa1          69 QLRHLVKAAQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQ  130 (264)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHhccccHHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCC
Confidence            44444333332222221111100111112233344455567777888888888888777643

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.05  E-value=0.00016  Score=64.67  Aligned_cols=115  Identities=9%  Similarity=-0.141  Sum_probs=64.8

Q ss_pred             ChhHHHHHHHhccc---CChhhHHHHHHHHHhcCCCCchHHHH----------HHHHHHHHhcccCChhhHHHHHHHHHh
Q 040338          247 STQKADLAFELMSR---RNMISWMVLISAFSQAGVLEKPRFFF----------FFVSLLSGCSHSGPVTKGKHYFTAMAK  313 (385)
Q Consensus       247 ~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~a~~~~----------~~~~l~~~~~~~~~~~~a~~~~~~~~~  313 (385)
                      .++.|+..+....+   ++...+..+...+.+.|+.++|...+          ++..+...+...|++++|...|++..+
T Consensus       101 ~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~  180 (497)
T d1ya0a1         101 FYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQ  180 (497)
T ss_dssp             HHHHHHHHHTC-------------------------------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            34444444443322   24456666777777777777776554          677788888888999999999999888


Q ss_pred             ccc--hhhHHHHHHHHHccCCHHHHHHHHHhCCCC--CCcchHHHHHHHHHh
Q 040338          314 FTY--TCYFVCMVDLLGLSGLLGEAKKLIDEMPSK--PTCVIWGALLGACCS  361 (385)
Q Consensus       314 ~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~li~~~~~  361 (385)
                      ..+  ...|+.+...+...|+..+|...|.+...-  |...++..|...+.+
T Consensus       181 l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~  232 (497)
T d1ya0a1         181 LVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSK  232 (497)
T ss_dssp             HCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHH
T ss_pred             HCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            888  788888999999999999998888776552  555566666665544

>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=96.92  E-value=0.0018  Score=47.45  Aligned_cols=89  Identities=8%  Similarity=-0.092  Sum_probs=66.3

Q ss_pred             HhcccCChhhHHHHHHHHHhccc--------------hhhHHHHHHHHHccCCHHHHHHHHHhCCC--------CCC---
Q 040338          294 GCSHSGPVTKGKHYFTAMAKFTY--------------TCYFVCMVDLLGLSGLLGEAKKLIDEMPS--------KPT---  348 (385)
Q Consensus       294 ~~~~~~~~~~a~~~~~~~~~~~~--------------~~~~~~li~~~~~~g~~~~A~~~~~~m~~--------~p~---  348 (385)
                      .+...|++++|+..|++......              ...|+.+..+|.+.|++++|.+-+++...        .++   
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~   97 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGK   97 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccc
Confidence            34456777777777777665333              35677889999999999999988877653        111   


Q ss_pred             --cchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          349 --CVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       349 --~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                        ...|..+..+|...|++++|+..|++.++..+..
T Consensus        98 ~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~~~  133 (156)
T d2hr2a1          98 LWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEER  133 (156)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHC
T ss_pred             hhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHh
Confidence              2357778899999999999999999988776543

>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=96.65  E-value=0.0013  Score=47.60  Aligned_cols=120  Identities=6%  Similarity=-0.063  Sum_probs=87.2

Q ss_pred             HcCCChhHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcccCChhhHHHHHHHHHhccc--h
Q 040338          243 AEGGSTQKADLAFELMSR--R-NMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGCSHSGPVTKGKHYFTAMAKFTY--T  317 (385)
Q Consensus       243 ~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~  317 (385)
                      -+.+.+++|+..|+...+  | +...+..+..++...+++..+.+-            .+.+++|+..|++..+..+  .
T Consensus         8 ~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~------------~~~~~~Ai~~~~kAl~l~P~~~   75 (145)
T d1zu2a1           8 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDA------------KQMIQEAITKFEEALLIDPKKD   75 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHH------------HHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHH------------HHHHHHHHHHHHHHHHhcchhh
Confidence            344578999999998865  4 667888888888887777665432            3457889999999998888  7


Q ss_pred             hhHHHHHHHHHccCC-----------HHHHHHHHHhCCC-CCCcchHHHHHHHHHhcCChHHHHHHHHHHHhccc
Q 040338          318 CYFVCMVDLLGLSGL-----------LGEAKKLIDEMPS-KPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDV  380 (385)
Q Consensus       318 ~~~~~li~~~~~~g~-----------~~~A~~~~~~m~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  380 (385)
                      ..|..+..+|...|+           +++|.+.|+...+ .|+...|..-+.-+      .+|.+++.+..+.|.
T Consensus        76 ~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1          76 EAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH------HTHHHHHHHHHHSSS
T ss_pred             HHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence            788888888876553           5778888887765 47776665554443      456677777666553

>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=96.64  E-value=0.018  Score=41.86  Aligned_cols=103  Identities=14%  Similarity=0.050  Sum_probs=71.6

Q ss_pred             hhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccC-CC----------chHHHhHHHHHHhcCChhHHHHHHHhccCCCc
Q 040338           50 FTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFV-SD----------ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSL  118 (385)
Q Consensus        50 ~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~-~~----------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~  118 (385)
                      .+|..+-.+... ...|++++|+..|++..+.... |+          ...|+.+..+|.+.|++++|..-+++..    
T Consensus         8 ~a~~~l~~g~~~-~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al----   82 (156)
T d2hr2a1           8 GAYLALSDAQRQ-LVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL----   82 (156)
T ss_dssp             HHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH----
T ss_pred             HHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhh----
Confidence            355555444332 1269999999999999875321 21          3578889999999999999998886643    


Q ss_pred             cccccchHHHHHHhcCCCC--C-----CcchHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          119 FCWKFGIIRLLIMFQKMPE--R-----DLVSWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       119 ~~~~~~~~~a~~~~~~~~~--~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                                 +++.+...  +     ...+|+.+..+|...|++++|+..|++..+
T Consensus        83 -----------~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          83 -----------HYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             -----------HHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----------hcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                       22222211  1     122567788899999999999999988764

>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=96.35  E-value=0.0023  Score=42.43  Aligned_cols=61  Identities=13%  Similarity=0.040  Sum_probs=42.8

Q ss_pred             HHHHHHHccCCHHHHHHHHHhCCCC--------CC-cchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          322 CMVDLLGLSGLLGEAKKLIDEMPSK--------PT-CVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       322 ~li~~~~~~g~~~~A~~~~~~m~~~--------p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      -+...+.+.|++++|+..|++..+.        ++ ..++..+..+|.+.|++++|+..++++++.+|..
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~   79 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEH   79 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCC
Confidence            4566677777777777777665431        11 3457778888888888888888888888777764

>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=96.34  E-value=0.0063  Score=48.79  Aligned_cols=119  Identities=11%  Similarity=-0.043  Sum_probs=77.0

Q ss_pred             cCCChHHHHHHHHHHHHcccchhhHHhhhhhHHHHHhhhCCCChhhHHHHHHHHHhhhccCChHHHHHHHHHHHHhccCC
Q 040338            6 SLKSLPIARKIHAQLISTCLISSIFLQLIDDDYRVFCDIGPRYLFTYNTMINGGVRCLCVGNIKMALHLHGLVKKFYFVS   85 (385)
Q Consensus         6 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~~~~a~~~~~~m~~~g~~~   85 (385)
                      +.|++++|...+++.++.                     .+.|...+..+...++.   .|++++|.+.++...+..  |
T Consensus         8 ~~G~l~eAl~~l~~al~~---------------------~P~d~~ar~~La~lL~~---~G~~e~A~~~l~~a~~l~--P   61 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKA---------------------SPKDASLRSSFIELLCI---DGDFERADEQLMQSIKLF--P   61 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHT---------------------CTTCHHHHHHHHHHHHH---HTCHHHHHHHHHHHHHHC--G
T ss_pred             HCCCHHHHHHHHHHHHHH---------------------CCCCHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHhC--C
Confidence            456677777777766663                     25578889999999888   899999999999999864  4


Q ss_pred             C-chHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCC-CcchHHHHHHHHHhCCCchHHHHHH
Q 040338           86 D-ESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPER-DLVSWNTMISILTRHGFGFETLCTF  163 (385)
Q Consensus        86 ~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~  163 (385)
                      + ...+..+...+...+..+++..-.   .....                ..+| +...+......+.+.|+.++|.+.+
T Consensus        62 ~~~~~~~~l~~ll~a~~~~~~a~~~~---~~~~~----------------~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~  122 (264)
T d1zbpa1          62 EYLPGASQLRHLVKAAQARKDFAQGA---ATAKV----------------LGENEELTKSLVSFNLSMVSQDYEQVSELA  122 (264)
T ss_dssp             GGHHHHHHHHHHHHHHHHHHHHTTSC---CCEEC----------------CCSCHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHhccccHHHHHHh---hhhhc----------------ccCchHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            3 444444444444333333322211   11111                0022 2333444556778899999999999


Q ss_pred             HHHHHC
Q 040338          164 IELWNH  169 (385)
Q Consensus       164 ~~m~~~  169 (385)
                      +++.+.
T Consensus       123 ~~a~e~  128 (264)
T d1zbpa1         123 LQIEEL  128 (264)
T ss_dssp             HHHHHH
T ss_pred             HHHHhc
Confidence            998775

>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=95.86  E-value=0.035  Score=36.28  Aligned_cols=78  Identities=8%  Similarity=-0.121  Sum_probs=56.7

Q ss_pred             CchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCC--CC-cchHHHHHHHHHhCCCchHHHHH
Q 040338           86 DESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPE--RD-LVSWNTMISILTRHGFGFETLCT  162 (385)
Q Consensus        86 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~~~~~~a~~~  162 (385)
                      +...+-.+...+.+.|++++|...|++..+               +...-+.  ++ ..+++.|..++.+.|++++|++.
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~---------------~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~   68 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALR---------------QLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLL   68 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---------------HHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHH
Confidence            455566788889999999999999876532               2222212  22 45788899999999999999999


Q ss_pred             HHHHHHCCCCCC-HhhHHH
Q 040338          163 FIELWNHGFGLS-SMLYAT  180 (385)
Q Consensus       163 ~~~m~~~g~~p~-~~t~~~  180 (385)
                      +++..+.  .|+ ..+++.
T Consensus        69 y~~aL~l--~P~~~~a~~N   85 (95)
T d1tjca_          69 TKKLLEL--DPEHQRANGN   85 (95)
T ss_dssp             HHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHh--CcCCHHHHHH
Confidence            9999884  564 344443

>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=95.69  E-value=0.17  Score=34.42  Aligned_cols=138  Identities=12%  Similarity=-0.099  Sum_probs=98.1

Q ss_pred             cCChHHHHHHHHHHHHhccCCCchHHHhHHHHHHhcCChhHHHHHHHhccCCCccccccchHHHHHHhcCCCCCCcchHH
Q 040338           65 VGNIKMALHLHGLVKKFYFVSDESIAKSSIDMHVKCGAVDYAESAFLRMLNPSLFCWKFGIIRLLIMFQKMPERDLVSWN  144 (385)
Q Consensus        65 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  144 (385)
                      .|.+++..++..+...+   .+..-||.+|.-....-+-+...++++.+-+.--.+.-+++.....-+-.+ ..+..-++
T Consensus        15 dG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~-n~~se~vd   90 (161)
T d1wy6a1          15 DGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVIN-NTLNEHVN   90 (161)
T ss_dssp             TTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHT-TCCCHHHH
T ss_pred             hhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHh-cchHHHHH
Confidence            58888888888888774   466677777777777777777777777664432222223333333333322 23344567


Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCC
Q 040338          145 TMISILTRHGFGFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPS  207 (385)
Q Consensus       145 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  207 (385)
                      ..++...+.|+-+.-.++++.+.+. -+|+....-.+..+|.+.|+..++.+++.+.-+.|.+
T Consensus        91 lALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          91 KALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            7889999999999999999997664 4677777888999999999999999999999998874

>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=95.28  E-value=0.23  Score=33.73  Aligned_cols=134  Identities=9%  Similarity=-0.064  Sum_probs=87.2

Q ss_pred             cCCChhHHHHHHHhccc-CChhhHHHHHHHHHhcCCCCchHHHHHHHHHHHHh--cccCChhhHHHHHHHHHhccc-hhh
Q 040338          244 EGGSTQKADLAFELMSR-RNMISWMVLISAFSQAGVLEKPRFFFFFVSLLSGC--SHSGPVTKGKHYFTAMAKFTY-TCY  319 (385)
Q Consensus       244 ~~g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~-~~~  319 (385)
                      -.|.+++..++..+..+ .+..-||-+|--....-+-+-..+++  ..+...+  ...+++......+   ...+. ...
T Consensus        14 ldG~ve~Gveii~k~~~ss~~~E~NW~ICNiidt~dC~~v~~~L--d~IG~~FDls~C~Nlk~vv~C~---~~~n~~se~   88 (161)
T d1wy6a1          14 LDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVL--DKIGSYFDLDKCQNLKSVVECG---VINNTLNEH   88 (161)
T ss_dssp             HTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHH--HHHGGGSCGGGCSCTHHHHHHH---HHTTCCCHH
T ss_pred             HhhhHHhHHHHHHHHcccCCccccceeeeecccccchHHHHHHH--HHHhhhcCchhhhcHHHHHHHH---HHhcchHHH
Confidence            45788888888888765 35555555554443333222222211  1111111  1123332222222   22233 677


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHhCCC--CCCcchHHHHHHHHHhcCChHHHHHHHHHHHhccccC
Q 040338          320 FVCMVDLLGLSGLLGEAKKLIDEMPS--KPTCVIWGALLGACCSHYNTKLAELVMRNLLQLDVKV  382 (385)
Q Consensus       320 ~~~li~~~~~~g~~~~A~~~~~~m~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  382 (385)
                      ++.-++.+..+|+-+...++++++.+  +|++...-.+.+||-+.|+..++-+++.+..+.|.+.
T Consensus        89 vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~Ke  153 (161)
T d1wy6a1          89 VNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEKE  153 (161)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHHH
Confidence            78889999999999999999999655  3888888889999999999999999999999998764

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=94.90  E-value=0.032  Score=39.13  Aligned_cols=86  Identities=12%  Similarity=-0.108  Sum_probs=66.9

Q ss_pred             ccCChhhHHHHHHHHHhccchhhHHHHHHHHHc----cCCHHHHHHHHHhCCCCCCcchHHHHHHHHHh----cCChHHH
Q 040338          297 HSGPVTKGKHYFTAMAKFTYTCYFVCMVDLLGL----SGLLGEAKKLIDEMPSKPTCVIWGALLGACCS----HYNTKLA  368 (385)
Q Consensus       297 ~~~~~~~a~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~----~g~~~~a  368 (385)
                      ...+.++|.+.+++..+.+.+.....|...|..    ..+.++|.++|+...+.-+......|...|..    ..+.++|
T Consensus        35 ~~~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~~g~~~a~~~Lg~~y~~G~gv~~d~~~A  114 (133)
T d1klxa_          35 SQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQA  114 (133)
T ss_dssp             TTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             cccCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHHHhhhhccCcchHHHHHHHHHHcCCccCCCHHHH
Confidence            345778899999999888886666666666654    56789999999998776666667777777766    4688999


Q ss_pred             HHHHHHHHhccccC
Q 040338          369 ELVMRNLLQLDVKV  382 (385)
Q Consensus       369 ~~~~~~~~~~~~~~  382 (385)
                      .+++++..+.|..+
T Consensus       115 ~~~~~~Aa~~G~~~  128 (133)
T d1klxa_         115 VKTFEKACRLGSED  128 (133)
T ss_dssp             HHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHCCCHH
Confidence            99999998887654

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=92.96  E-value=0.85  Score=31.29  Aligned_cols=17  Identities=0%  Similarity=0.038  Sum_probs=8.3

Q ss_pred             CccchhhHHHHHHHhCC
Q 040338          190 DLEWGPHLHSRVVHMEP  206 (385)
Q Consensus       190 ~~~~a~~~~~~~~~~~~  206 (385)
                      +.++|.+.++...+.|.
T Consensus       110 d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_         110 NEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             CHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHCCC
Confidence            44455555555544443

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=91.55  E-value=3.5  Score=34.92  Aligned_cols=90  Identities=8%  Similarity=-0.097  Sum_probs=63.2

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhccc-hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcc--hHHHHHHHHHhcCC
Q 040338          288 FVSLLSGCSHSGPVTKGKHYFTAMAKFTY-TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCV--IWGALLGACCSHYN  364 (385)
Q Consensus       288 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~--~~~~li~~~~~~g~  364 (385)
                      ...+.......+..+.+...+......+. .....-.+......+++..+...+..|...|...  -.-=+..++...|+
T Consensus       255 ~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~w~~~~al~~~~~~~~~~~~~~l~~~~~~~~r~~YW~gRa~~~~G~  334 (450)
T d1qsaa1         255 RDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQADLLLERGR  334 (450)
T ss_dssp             HHHHHHTSCSTTCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTTGGGSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCchHHHHHHHHhhcccccchHHHHHHHHHHHHcCChHHHHHHHHhcCcccccHHHHHHHHHHHHHHcCC
Confidence            33444455566777788887777666555 3333445555667899999999999998754332  22346688999999


Q ss_pred             hHHHHHHHHHHHh
Q 040338          365 TKLAELVMRNLLQ  377 (385)
Q Consensus       365 ~~~a~~~~~~~~~  377 (385)
                      .+.|..+|..+..
T Consensus       335 ~~~A~~~~~~~a~  347 (450)
T d1qsaa1         335 EAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             hhhHHHHHHHHhc
Confidence            9999999998764

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=89.91  E-value=4.9  Score=33.91  Aligned_cols=134  Identities=10%  Similarity=-0.078  Sum_probs=76.8

Q ss_pred             HHHHHHcCCChhHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCchHHHH-------HHHHHHHHhcccCC-hhhHHH
Q 040338          238 LVTMYAEGGSTQKADLAFELMSRR---NMISWMVLISAFSQAGVLEKPRFFF-------FFVSLLSGCSHSGP-VTKGKH  306 (385)
Q Consensus       238 li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~a~~~~-------~~~~l~~~~~~~~~-~~~a~~  306 (385)
                      .+......+++..+...++.|...   ...-..-+..++...|+.+.|...|       +|--++.+- +.|. +.-...
T Consensus       291 ~~~~al~~~~~~~~~~~~~~l~~~~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~~~~fYG~LAa~-~Lg~~~~~~~~  369 (450)
T d1qsaa1         291 RVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQADLLLERGREAEAKEILHQLMQQRGFYPMVAAQ-RIGEEYELKID  369 (450)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHSCTTGGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSHHHHHHHH-HTTCCCCCCCC
T ss_pred             HHHHHHHcCChHHHHHHHHhcCcccccHHHHHHHHHHHHHHcCChhhHHHHHHHHhcCCChHHHHHHH-HcCCCCCCCcC
Confidence            444445567788888888777642   2233345667777777777777666       222111111 1111 000000


Q ss_pred             HHHHHHhccc-----hhhHHHHHHHHHccCCHHHHHHHHHhCCCCCCcchHHHHHHHHHhcCChHHHHHHHHHHH
Q 040338          307 YFTAMAKFTY-----TCYFVCMVDLLGLSGLLGEAKKLIDEMPSKPTCVIWGALLGACCSHYNTKLAELVMRNLL  376 (385)
Q Consensus       307 ~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  376 (385)
                         . .....     ...-...+..+...|+..+|...+..+..+.+......+.....+.|.++.|+....+..
T Consensus       370 ---~-~~~~~~~~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l~~~~~~~~~~~la~lA~~~g~~~~aI~a~~~~~  440 (450)
T d1qsaa1         370 ---K-APQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLVKSKSKTEQAQLARYAFNNQWWDLSVQATIAGK  440 (450)
T ss_dssp             ---C-CCSCCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHTT
T ss_pred             ---C-CCccHHHhhhcChHHHHHHHHHHcCCchHHHHHHHHHHhCCCHHHHHHHHHHHHHCCChhHHHHHHHHHH
Confidence               0 00000     111112456677889999999988877766566677778888888999999888776653

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.36  E-value=0.97  Score=30.58  Aligned_cols=27  Identities=7%  Similarity=-0.214  Sum_probs=15.6

Q ss_pred             hHHHHHHHHHhCCCchHHHHHHHHHHH
Q 040338          142 SWNTMISILTRHGFGFETLCTFIELWN  168 (385)
Q Consensus       142 ~~~~li~~~~~~~~~~~a~~~~~~m~~  168 (385)
                      .+-.|.-+|.+.|++++|.+.++.+.+
T Consensus        75 ~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          75 CLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            334444455566666666666666655

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.33  E-value=0.61  Score=31.63  Aligned_cols=54  Identities=11%  Similarity=-0.044  Sum_probs=42.1

Q ss_pred             hccCChHHHHHHHHHHHHhccCCC-chHHHhHHHHHHhcCChhHHHHHHHhccCCC
Q 040338           63 LCVGNIKMALHLHGLVKKFYFVSD-ESIAKSSIDMHVKCGAVDYAESAFLRMLNPS  117 (385)
Q Consensus        63 ~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  117 (385)
                      ....++++++.+++++.+.+ +.+ ...+--|.-+|.+.|++++|.+.++.+.+.+
T Consensus        49 ~~~~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ie  103 (124)
T d2pqrb1          49 TDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  103 (124)
T ss_dssp             SCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccC
Confidence            34577889999999998764 223 3566677788999999999999998886654

>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=85.19  E-value=1.6  Score=27.84  Aligned_cols=61  Identities=11%  Similarity=-0.023  Sum_probs=45.7

Q ss_pred             chHHHHHHHHHHHCCCCCCHhhHHHHHHHhcCccCccchhhHHHHHHHhCCCCchHHHHHHH
Q 040338          156 GFETLCTFIELWNHGFGLSSMLYATAFSARASVYDLEWGPHLHSRVVHMEPSLDVFVGSGLI  217 (385)
Q Consensus       156 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  217 (385)
                      .-+..+-+..+....+.|+.....+.+++|.+.+|+..|.++++-++...- ++...|.-++
T Consensus        22 ~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~-~~k~~y~yil   82 (105)
T d1v54e_          22 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG-PHKEIYPYVI   82 (105)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT-TCTTHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc-CcHHHHHHHH
Confidence            345666777777778899999999999999999999999999998876532 2344554443