Citrus Sinensis ID: 047113

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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-----
Protein Sequence
MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL
Secondary Structure (PSIPRED)
ccHHHHHHcccccccEEEHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccccccHHHHHHHHcccccccHHHHHHHHHHHHHccccHHHHHHHHHcHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHcccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEEEc
Coil and Loop (DISEMBL)
mddaerifggiidknvVIWSGMIASHAIHGQEREALEAFYLVIHcsdgkpnnvTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDllatgetepyVWGALLGACRihhnvkigelvakdpfhldpkndayytsl
Flexible Loop (DISEMBL)
mddaerifggiidknvvIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGElvakdpfhldpkndayytsl
Low Complexity Region (SEG)
MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL
Disordered region (IsUnstruct)
*****RIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHL***********
Disordered Region (DISOPRED)
MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL
Disordered Region (DISEMBL)
MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL
Disordered Region (DISPRO)
MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL
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	145	2.2.26 [Sep-21-2011]
Q9SS97	660	Putative pentatricopeptid	yes	no	0.979	0.215	0.433	8e-32
Q9STF3	657	Pentatricopeptide repeat-	no	no	0.993	0.219	0.362	6e-26
Q9FFG8	657	Pentatricopeptide repeat-	no	no	0.937	0.207	0.410	7e-26
Q9SUH6	792	Pentatricopeptide repeat-	no	no	0.979	0.179	0.373	2e-25
Q9SN39	871	Pentatricopeptide repeat-	no	no	0.951	0.158	0.383	3e-25
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.910	0.212	0.392	8e-25
Q5G1T1	850	Pentatricopeptide repeat-	no	no	0.993	0.169	0.375	4e-24
P0C8Q2	654	Pentatricopeptide repeat-	no	no	0.979	0.217	0.386	8e-24
Q9LTV8	694	Pentatricopeptide repeat-	no	no	0.986	0.206	0.35	1e-23
Q9FLZ9	677	Pentatricopeptide repeat-	no	no	0.993	0.212	0.365	2e-23

>sp|Q9SS97|PP205_ARATH Putative pentatricopeptide repeat-containing protein At3g01580 OS=Arabidopsis thaliana GN=PCMP-E87 PE=3 SV=2

 Score =  135 bits (340), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 68/157 (43%), Positives = 99/157 (63%), Gaps = 15/157 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           + +A ++F GI  K+ V+W+ +I  + IHG+  +ALE F  ++  S+ KPN VTFLSIL 
Sbjct: 417 LGNASKVFNGIALKDTVVWTSLITGYGIHGKGTKALETFNHMVKSSEVKPNEVTFLSILS 476

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGETE--------------P 105
           ACS++GLI EG+++F +MV+D++L  NLEHY + VDLL   G+ +              P
Sbjct: 477 ACSHAGLIHEGLRIFKLMVNDYRLAPNLEHYAVLVDLLGRVGDLDTAIEITKRMPFSPTP 536

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
            + G LLGACRIH N ++ E VAK  F L+  +  YY
Sbjct: 537 QILGTLLGACRIHQNGEMAETVAKKLFELESNHAGYY 573

Arabidopsis thaliana (taxid: 3702)

>sp|Q9STF3|PP265_ARATH Pentatricopeptide repeat-containing protein At3g46790, chloroplastic OS=Arabidopsis thaliana GN=CRR2 PE=2 SV=1

 Score =  115 bits (289), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 58/160 (36%), Positives = 93/160 (58%), Gaps = 16/160 (10%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           ++  +R+F  + D++VV W+ +I+S+ +HG  ++A++ F  ++  +   P  VTF+S+L 
Sbjct: 336 LEVGQRVFDRMHDRDVVSWNSLISSYGVHGYGKKAIQIFEEML-ANGASPTPVTFVSVLG 394

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG---------------ETEP 105
           ACS+ GL+EEG ++F+ M  D  +   +EHY   VDLL                  E  P
Sbjct: 395 ACSHEGLVEEGKRLFETMWRDHGIKPQIEHYACMVDLLGRANRLDEAAKMVQDMRTEPGP 454

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
            VWG+LLG+CRIH NV++ E  ++  F L+PKN   Y  L
Sbjct: 455 KVWGSLLGSCRIHGNVELAERASRRLFALEPKNAGNYVLL 494

Required for the intergenic processing between chloroplast rsp7 and ndhB transcripts.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FFG8|PP417_ARATH Pentatricopeptide repeat-containing protein At5g44230 OS=Arabidopsis thaliana GN=PCMP-H17 PE=2 SV=1

 Score =  115 bits (289), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 62/151 (41%), Positives = 90/151 (59%), Gaps = 15/151 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           +++A  +F  + +KNV  +S MI   A HG+ +EAL  F+ ++  ++ KPN VTF+  L 
Sbjct: 334 VEEAVNVFMSMNNKNVFTYSSMILGLATHGRAQEALHLFHYMVTQTEIKPNTVTFVGALM 393

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-------------TGETEPY- 106
           ACS+SGL+++G +VFD M   F +    +HY   VDLL              T   EP+ 
Sbjct: 394 ACSHSGLVDQGRQVFDSMYQTFGVQPTRDHYTCMVDLLGRTGRLQEALELIKTMSVEPHG 453

Query: 107 -VWGALLGACRIHHNVKIGELVAKDPFHLDP 136
            VWGALLGACRIH+N +I E+ A+  F L+P
Sbjct: 454 GVWGALLGACRIHNNPEIAEIAAEHLFELEP 484

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SUH6|PP341_ARATH Pentatricopeptide repeat-containing protein At4g30700 OS=Arabidopsis thaliana GN=DYW9 PE=2 SV=1

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/158 (37%), Positives = 91/158 (57%), Gaps = 16/158 (10%)

Query: 3   DAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFAC 62
           +A R+F  +  KN V W+ MI+ + +HGQ +EAL  FY +++ S   P  VTFL +L+AC
Sbjct: 473 EARRLFDLMTKKNEVTWNTMISGYGLHGQGQEALNIFYEMLN-SGITPTPVTFLCVLYAC 531

Query: 63  SYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------ETEP--YV 107
           S++GL++EG ++F+ M+H +  + +++HY   VD+L                  EP   V
Sbjct: 532 SHAGLVKEGDEIFNSMIHRYGFEPSVKHYACMVDILGRAGHLQRALQFIEAMSIEPGSSV 591

Query: 108 WGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           W  LLGACRIH +  +   V++  F LDP N  Y+  L
Sbjct: 592 WETLLGACRIHKDTNLARTVSEKLFELDPDNVGYHVLL 629

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN39|PP320_ARATH Pentatricopeptide repeat-containing protein At4g18750, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H45 PE=2 SV=1

 Score =  113 bits (283), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 59/154 (38%), Positives = 96/154 (62%), Gaps = 16/154 (10%)

Query: 4   AERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACS 63
           A  +F  I  K++V W+ MIA + +HG  +EA+ A +  +  +  + + ++F+S+L+ACS
Sbjct: 553 AHMLFDDIASKDLVSWTVMIAGYGMHGFGKEAI-ALFNQMRQAGIEADEISFVSLLYACS 611

Query: 64  YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGE--------------TEPYVW 108
           +SGL++EG + F+IM H+ +++  +EHY   VD+LA TG+               +  +W
Sbjct: 612 HSGLVDEGWRFFNIMRHECKIEPTVEHYACIVDMLARTGDLIKAYRFIENMPIPPDATIW 671

Query: 109 GALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
           GALL  CRIHH+VK+ E VA+  F L+P+N  YY
Sbjct: 672 GALLCGCRIHHDVKLAEKVAEKVFELEPENTGYY 705

Arabidopsis thaliana (taxid: 3702)

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

 Score =  112 bits (280), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 60/153 (39%), Positives = 86/153 (56%), Gaps = 21/153 (13%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           M++A  +F  I  K+V  W+ +I+ +A HG  REA+  F + +     KPN +TF ++L 
Sbjct: 298 MEEALEVFKNIKKKSVQAWTALISGYAYHGHGREAISKF-MEMQKMGIKPNVITFTAVLT 356

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG---------------ETEP 105
           ACSY+GL+EEG  +F  M  D+ L   +EHYG  VDLL                  +   
Sbjct: 357 ACSYTGLVEEGKLIFYSMERDYNLKPTIEHYGCIVDLLGRAGLLDEAKRFIQEMPLKPNA 416

Query: 106 YVWGALLGACRIHHNVKIGE-----LVAKDPFH 133
            +WGALL ACRIH N+++GE     L+A DP+H
Sbjct: 417 VIWGALLKACRIHKNIELGEEIGEILIAIDPYH 449

Arabidopsis thaliana (taxid: 3702)

>sp|Q5G1T1|PP272_ARATH Pentatricopeptide repeat-containing protein At3g49170, chloroplastic OS=Arabidopsis thaliana GN=EMB2261 PE=2 SV=1

 Score =  109 bits (273), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 84/160 (52%), Gaps = 16/160 (10%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           +D A R+F  + ++NV+ W+ MI   A HG     LE F  +I     KPN VT+++IL 
Sbjct: 525 IDTASRVFNFMENRNVISWTSMITGFAKHGFAIRVLETFNQMIE-EGVKPNEVTYVAILS 583

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG----------ETEPY---- 106
           ACS+ GL+ EG + F+ M  D ++   +EHY   VDLL              T P+    
Sbjct: 584 ACSHVGLVSEGWRHFNSMYEDHKIKPKMEHYACMVDLLCRAGLLTDAFEFINTMPFQADV 643

Query: 107 -VWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
            VW   LGACR+H N ++G+L A+    LDP   A Y  L
Sbjct: 644 LVWRTFLGACRVHSNTELGKLAARKILELDPNEPAAYIQL 683

May play a role in embryogenesis.

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8Q2|PP323_ARATH Pentatricopeptide repeat-containing protein At4g19191, mitochondrial OS=Arabidopsis thaliana GN=PCMP-E1 PE=2 SV=1

 Score =  108 bits (271), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 91/158 (57%), Gaps = 16/158 (10%)

Query: 3   DAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFAC 62
           +A  IF    +K VV W+ MIA +A++G   EAL+ F  +I   D KPN++TFL++L AC
Sbjct: 411 EARDIFDNTPEKTVVTWTTMIAGYALNGIFLEALKLFSKMIDL-DYKPNHITFLAVLQAC 469

Query: 63  SYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA---------------TGETEPYV 107
           ++SG +E+G + F IM   + +   L+HY   VDLL                + + +  +
Sbjct: 470 AHSGSLEKGWEYFHIMKQVYNISPGLDHYSCMVDLLGRKGKLEEALELIRNMSAKPDAGI 529

Query: 108 WGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           WGALL AC+IH NVKI E  A+  F+L+P+  A Y  +
Sbjct: 530 WGALLNACKIHRNVKIAEQAAESLFNLEPQMAAPYVEM 567

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LTV8|PP224_ARATH Pentatricopeptide repeat-containing protein At3g12770 OS=Arabidopsis thaliana GN=PCMP-H43 PE=2 SV=1

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 56/160 (35%), Positives = 89/160 (55%), Gaps = 17/160 (10%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           ++ A  +F   +D++VV+WS MI  + +HG+ REA+ + Y  +      PN+VTFL +L 
Sbjct: 374 VEGARLVFDRTLDRDVVVWSAMIVGYGLHGRAREAI-SLYRAMERGGVHPNDVTFLGLLM 432

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------ETEP-- 105
           AC++SG++ EG   F+ M  D +++   +HY   +DLL                  +P  
Sbjct: 433 ACNHSGMVREGWWFFNRMA-DHKINPQQQHYACVIDLLGRAGHLDQAYEVIKCMPVQPGV 491

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
            VWGALL AC+ H +V++GE  A+  F +DP N  +Y  L
Sbjct: 492 TVWGALLSACKKHRHVELGEYAAQQLFSIDPSNTGHYVQL 531

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLZ9|PP405_ARATH Pentatricopeptide repeat-containing protein At5g39350 OS=Arabidopsis thaliana GN=PCMP-E16 PE=2 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 86/164 (52%), Gaps = 20/164 (12%)

Query: 1   MDDAERIFGGIIDK----NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFL 56
           ++ A +IF GI +K    +VV+W  +I+ + +HG    AL+ F  ++  S   PN +TF 
Sbjct: 471 LESAHKIFNGIQEKHKSKDVVLWGALISGYGMHGDGHNALQVFMEMVR-SGVTPNEITFT 529

Query: 57  SILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG--------------- 101
           S L ACS+SGL+EEG+ +F  M+  ++      HY   VDLL                  
Sbjct: 530 SALNACSHSGLVEEGLTLFRFMLEHYKTLARSNHYTCIVDLLGRAGRLDEAYNLITTIPF 589

Query: 102 ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           E    VWGALL AC  H NV++GE+ A   F L+P+N   Y  L
Sbjct: 590 EPTSTVWGALLAACVTHENVQLGEMAANKLFELEPENTGNYVLL 633

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	145
356514095	700	PREDICTED: putative pentatricopeptide re	1.0	0.207	0.537	2e-39
359488803	1291	PREDICTED: putative pentatricopeptide re	1.0	0.112	0.525	1e-38
357468777	838	hypothetical protein MTR_4g015760 [Medic	1.0	0.173	0.518	2e-38
356514087	701	PREDICTED: putative pentatricopeptide re	1.0	0.206	0.518	3e-37
297828580	638	predicted protein [Arabidopsis lyrata su	0.979	0.222	0.433	4e-30
6016735	641	hypothetical protein [Arabidopsis thalia	0.979	0.221	0.433	5e-30
334185017	660	pentatricopeptide repeat-containing prot	0.979	0.215	0.433	5e-30
296082284	581	unnamed protein product [Vitis vinifera]	0.972	0.242	0.445	3e-29
359488559	735	PREDICTED: pentatricopeptide repeat-cont	0.972	0.191	0.445	4e-29
449492963	1725	PREDICTED: uncharacterized protein LOC10	0.972	0.081	0.414	4e-28

>gi|356514095|ref|XP_003525742.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g01580-like [Glycine max]

 Score =  166 bits (421), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/160 (53%), Positives = 112/160 (70%), Gaps = 15/160 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           +D+A ++F G+  K+VV WS +IA++  HGQ  EAL+ FY + + SD KPN+VTF+SIL 
Sbjct: 460 IDNANKVFKGMRRKDVVTWSSIIAAYGFHGQGEEALKLFYQMSNHSDVKPNDVTFVSILS 519

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT-GETE--------------P 105
           ACS++GLIEEGIK+F +MV+++QL  N EHYGI VDLL   GE +              P
Sbjct: 520 ACSHAGLIEEGIKMFHVMVNEYQLMPNTEHYGIMVDLLGRMGELDKALDMINEMPMQAGP 579

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           +VWGALLGACRIH N+KIGEL A + F LDP +  YYT L
Sbjct: 580 HVWGALLGACRIHQNIKIGELAALNLFLLDPNHAGYYTLL 619

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488803|ref|XP_002272525.2| PREDICTED: putative pentatricopeptide repeat-containing protein At5g09950 [Vitis vinifera]

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 84/160 (52%), Positives = 111/160 (69%), Gaps = 15/160 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           + DA ++F G+I ++VVIWS MIA++ IHG+  EALE F  ++  S  +PNNVTFLSIL 
Sbjct: 459 LGDAVKLFKGMIVRDVVIWSSMIAAYGIHGRGGEALEIFDQMVKNSTVRPNNVTFLSILS 518

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT-GE--------------TEP 105
           ACS++GL+EEG+K+FD MVHD+QL  + EH+GI VDLL   G+                P
Sbjct: 519 ACSHAGLVEEGLKIFDRMVHDYQLRPDSEHFGIMVDLLGRIGQLGKAMDIINRMPIPAGP 578

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           +VWGALLGACRIHHN+++GE  AK+ F LDP +  YY  L
Sbjct: 579 HVWGALLGACRIHHNIEMGEAAAKNLFWLDPSHAGYYILL 618

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357468777|ref|XP_003604673.1| hypothetical protein MTR_4g015760 [Medicago truncatula] gi|355505728|gb|AES86870.1| hypothetical protein MTR_4g015760 [Medicago truncatula]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 83/160 (51%), Positives = 109/160 (68%), Gaps = 15/160 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           ++DA ++F G+  K+VV WS +IA++  HGQ  EAL+ FY + + SD KPNNVTF+SIL 
Sbjct: 597 IEDANKVFKGMTYKDVVTWSSIIAAYGFHGQGEEALKLFYQMANHSDTKPNNVTFISILS 656

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT-GETE--------------P 105
           ACS+SGLI+EGI +FDIMV+ ++L  N EHY I VDLL   GE +              P
Sbjct: 657 ACSHSGLIKEGINMFDIMVNKYKLKPNSEHYAIMVDLLGRMGELDMALDVINNMPMQAGP 716

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
            +WGALLGACRIH N+K+GE+ AK+ F LDP +  YY  L
Sbjct: 717 DIWGALLGACRIHQNIKMGEVAAKNLFSLDPNHAGYYILL 756

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514087|ref|XP_003525738.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g01580-like [Glycine max]

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 83/160 (51%), Positives = 111/160 (69%), Gaps = 15/160 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           +D+A ++F G+   +VV WS +IA++  HGQ  EAL+  + + + SD KPN+VTF+SIL 
Sbjct: 459 IDNANKVFKGLRHTDVVTWSSIIAAYGFHGQGEEALKLSHQMSNHSDVKPNDVTFVSILS 518

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT-GETE--------------P 105
           ACS++GLIEEGIK+F +MV+++QL  N+EHYGI VDLL   GE +              P
Sbjct: 519 ACSHAGLIEEGIKMFHVMVNEYQLMPNIEHYGIMVDLLGRMGELDKALDMINNMPMQAGP 578

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           +VWGALLGACRIH N+KIGEL A + F LDP +  YYT L
Sbjct: 579 HVWGALLGACRIHQNIKIGELAALNLFLLDPNHAGYYTLL 618

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297828580|ref|XP_002882172.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297328012|gb|EFH58431.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 68/157 (43%), Positives = 99/157 (63%), Gaps = 15/157 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           + +A ++F  I  K+ V+W+ +I  + IHG+  +ALE F  ++  S+ KPN VTFLSIL 
Sbjct: 398 LGNASKVFNEIALKDTVVWTSLITGYGIHGKGTKALETFNHMVRSSEVKPNEVTFLSILS 457

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGETE--------------P 105
           ACS++GLI EG+++F++MV+D++L  NLEHY + VDLL   GE +              P
Sbjct: 458 ACSHAGLIHEGLRIFELMVNDYRLAPNLEHYAVLVDLLGRVGELDTAIEITKRMPFSPTP 517

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
            + G LLGACRIH N ++ E VAK  F L+  +  YY
Sbjct: 518 QILGTLLGACRIHQNGEMAETVAKQLFELESNHAGYY 554

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6016735|gb|AAF01561.1|AC009325_31 hypothetical protein [Arabidopsis thaliana]

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 68/157 (43%), Positives = 99/157 (63%), Gaps = 15/157 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           + +A ++F GI  K+ V+W+ +I  + IHG+  +ALE F  ++  S+ KPN VTFLSIL 
Sbjct: 398 LGNASKVFNGIALKDTVVWTSLITGYGIHGKGTKALETFNHMVKSSEVKPNEVTFLSILS 457

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGETE--------------P 105
           ACS++GLI EG+++F +MV+D++L  NLEHY + VDLL   G+ +              P
Sbjct: 458 ACSHAGLIHEGLRIFKLMVNDYRLAPNLEHYAVLVDLLGRVGDLDTAIEITKRMPFSPTP 517

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
            + G LLGACRIH N ++ E VAK  F L+  +  YY
Sbjct: 518 QILGTLLGACRIHQNGEMAETVAKKLFELESNHAGYY 554

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185017|ref|NP_186807.2| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|218546765|sp|Q9SS97.2|PP205_ARATH RecName: Full=Putative pentatricopeptide repeat-containing protein At3g01580 gi|332640170|gb|AEE73691.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 68/157 (43%), Positives = 99/157 (63%), Gaps = 15/157 (9%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           + +A ++F GI  K+ V+W+ +I  + IHG+  +ALE F  ++  S+ KPN VTFLSIL 
Sbjct: 417 LGNASKVFNGIALKDTVVWTSLITGYGIHGKGTKALETFNHMVKSSEVKPNEVTFLSILS 476

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGETE--------------P 105
           ACS++GLI EG+++F +MV+D++L  NLEHY + VDLL   G+ +              P
Sbjct: 477 ACSHAGLIHEGLRIFKLMVNDYRLAPNLEHYAVLVDLLGRVGDLDTAIEITKRMPFSPTP 536

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
            + G LLGACRIH N ++ E VAK  F L+  +  YY
Sbjct: 537 QILGTLLGACRIHQNGEMAETVAKKLFELESNHAGYY 573

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296082284|emb|CBI21289.3| unnamed protein product [Vitis vinifera]

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 70/157 (44%), Positives = 95/157 (60%), Gaps = 16/157 (10%)

Query: 4   AERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACS 63
           A + F  + +KNV  WS M+A + +HG  +EALE FY  ++ +  KPN +TF+S+L ACS
Sbjct: 263 ARKAFDRMREKNVKSWSAMVAGYGMHGHAKEALEVFY-EMNMAGVKPNYITFVSVLAACS 321

Query: 64  YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------ETEP--YVW 108
           ++GL+EEG   F  M H+F ++  +EHYG  VDLL                +  P   VW
Sbjct: 322 HAGLLEEGWHWFKAMSHEFDVEPGVEHYGCMVDLLGRAGYLKEAFDLIKGMKLRPDFVVW 381

Query: 109 GALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           GALLGACR+H NV +GE+ A+  F LDPKN  YY  L
Sbjct: 382 GALLGACRMHKNVDLGEISARKLFELDPKNCGYYVLL 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488559|ref|XP_002275581.2| PREDICTED: pentatricopeptide repeat-containing protein At3g26782, mitochondrial-like [Vitis vinifera]

 Score =  132 bits (333), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 70/157 (44%), Positives = 95/157 (60%), Gaps = 16/157 (10%)

Query: 4   AERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACS 63
           A + F  + +KNV  WS M+A + +HG  +EALE FY  ++ +  KPN +TF+S+L ACS
Sbjct: 417 ARKAFDRMREKNVKSWSAMVAGYGMHGHAKEALEVFY-EMNMAGVKPNYITFVSVLAACS 475

Query: 64  YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------ETEP--YVW 108
           ++GL+EEG   F  M H+F ++  +EHYG  VDLL                +  P   VW
Sbjct: 476 HAGLLEEGWHWFKAMSHEFDVEPGVEHYGCMVDLLGRAGYLKEAFDLIKGMKLRPDFVVW 535

Query: 109 GALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           GALLGACR+H NV +GE+ A+  F LDPKN  YY  L
Sbjct: 536 GALLGACRMHKNVDLGEISARKLFELDPKNCGYYVLL 572

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449492963|ref|XP_004159154.1| PREDICTED: uncharacterized protein LOC101226880 [Cucumis sativus]

 Score =  129 bits (324), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 65/157 (41%), Positives = 96/157 (61%), Gaps = 16/157 (10%)

Query: 4    AERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACS 63
            A++ F  + +KNV  W+ M+A + +HG+ +EAL+ FY ++  +  KPN +TF+S+L ACS
Sbjct: 1407 AKKTFDRMKEKNVKSWTAMVAGYGMHGRAKEALDIFYKMVR-AGVKPNYITFVSVLAACS 1465

Query: 64   YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------ETEP--YVW 108
            ++GL+EEG   F+ M H + ++  +EHYG  VDL                 + +P   VW
Sbjct: 1466 HAGLVEEGWHWFNAMKHKYDIEPGIEHYGCMVDLFGRAGCLNEAYNLIKRMKMKPDFVVW 1525

Query: 109  GALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
            G+LLGACRIH NV +GE+ A+  F LDP N  YY  L
Sbjct: 1526 GSLLGACRIHKNVDLGEIAAQKLFELDPDNCGYYVLL 1562

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	145
TAIR|locus:2167593	657	AT5G44230 [Arabidopsis thalian	0.937	0.207	0.417	1.3e-23
TAIR|locus:2124137	871	DOT4 "DEFECTIVELY ORGANIZED TR	0.951	0.158	0.396	1.8e-23
TAIR|locus:2102852	657	CRR2 "AT3G46790" [Arabidopsis	0.993	0.219	0.368	5.8e-23
TAIR|locus:2131939	792	MEF29 "AT4G30700" [Arabidopsis	0.979	0.179	0.373	1.4e-22
TAIR|locus:4515103421	654	AT4G19191 "AT4G19191" [Arabido	0.979	0.217	0.398	8.9e-22
TAIR|locus:2154855	620	AT5G66520 "AT5G66520" [Arabido	0.972	0.227	0.375	1e-21
TAIR|locus:2175653	677	AT5G39350 "AT5G39350" [Arabido	0.993	0.212	0.378	1.2e-21
TAIR|locus:2170548	608	AT5G40410 [Arabidopsis thalian	0.993	0.236	0.368	2.6e-21
TAIR|locus:2082886	850	EMB2261 "embryo defective 2261	0.986	0.168	0.378	3.1e-21
TAIR|locus:2102514	581	AT3G56550 [Arabidopsis thalian	0.972	0.242	0.343	6.3e-21

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

 Score = 280 (103.6 bits), Expect = 1.3e-23, P = 1.3e-23
 Identities = 63/151 (41%), Positives = 91/151 (60%)

Query:     1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
             +++A  +F  + +KNV  +S MI   A HG+ +EAL  F+ ++  ++ KPN VTF+  L 
Sbjct:   334 VEEAVNVFMSMNNKNVFTYSSMILGLATHGRAQEALHLFHYMVTQTEIKPNTVTFVGALM 393

Query:    61 ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGE------------TEPY- 106
             ACS+SGL+++G +VFD M   F +    +HY   VDLL  TG              EP+ 
Sbjct:   394 ACSHSGLVDQGRQVFDSMYQTFGVQPTRDHYTCMVDLLGRTGRLQEALELIKTMSVEPHG 453

Query:   107 -VWGALLGACRIHHNVKIGELVAKDPFHLDP 136
              VWGALLGACRIH+N +I E+ A+  F L+P
Sbjct:   454 GVWGALLGACRIHNNPEIAEIAAEHLFELEP 484

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2124137 DOT4 "DEFECTIVELY ORGANIZED TRIBUTARIES 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 281 (104.0 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 61/154 (39%), Positives = 96/154 (62%)

Query:     4 AERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACS 63
             A  +F  I  K++V W+ MIA + +HG  +EA+ A +  +  +  + + ++F+S+L+ACS
Sbjct:   553 AHMLFDDIASKDLVSWTVMIAGYGMHGFGKEAI-ALFNQMRQAGIEADEISFVSLLYACS 611

Query:    64 YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TG---------ETEPY-----VW 108
             +SGL++EG + F+IM H+ +++  +EHY   VD+LA TG         E  P      +W
Sbjct:   612 HSGLVDEGWRFFNIMRHECKIEPTVEHYACIVDMLARTGDLIKAYRFIENMPIPPDATIW 671

Query:   109 GALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
             GALL  CRIHH+VK+ E VA+  F L+P+N  YY
Sbjct:   672 GALLCGCRIHHDVKLAEKVAEKVFELEPENTGYY 705

GO:0009507 "chloroplast" evidence=ISM

GO:0010087 "phloem or xylem histogenesis" evidence=IMP

GO:0010305 "leaf vascular tissue pattern formation" evidence=IMP

GO:0010588 "cotyledon vascular tissue pattern formation" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2102852 CRR2 "AT3G46790" [Arabidopsis thaliana (taxid:3702)]

 Score = 274 (101.5 bits), Expect = 5.8e-23, P = 5.8e-23
 Identities = 59/160 (36%), Positives = 94/160 (58%)

Query:     1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
             ++  +R+F  + D++VV W+ +I+S+ +HG  ++A++ F  ++  +   P  VTF+S+L 
Sbjct:   336 LEVGQRVFDRMHDRDVVSWNSLISSYGVHGYGKKAIQIFEEML-ANGASPTPVTFVSVLG 394

Query:    61 ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGE-------------TEP-- 105
             ACS+ GL+EEG ++F+ M  D  +   +EHY   VDLL                 TEP  
Sbjct:   395 ACSHEGLVEEGKRLFETMWRDHGIKPQIEHYACMVDLLGRANRLDEAAKMVQDMRTEPGP 454

Query:   106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
              VWG+LLG+CRIH NV++ E  ++  F L+PKN   Y  L
Sbjct:   455 KVWGSLLGSCRIHGNVELAERASRRLFALEPKNAGNYVLL 494

GO:0009507 "chloroplast" evidence=ISS

GO:0031425 "chloroplast RNA processing" evidence=IMP

GO:0031426 "polycistronic mRNA processing" evidence=IMP

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2131939 MEF29 "AT4G30700" [Arabidopsis thaliana (taxid:3702)]

 Score = 272 (100.8 bits), Expect = 1.4e-22, P = 1.4e-22
 Identities = 59/158 (37%), Positives = 91/158 (57%)

Query:     3 DAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFAC 62
             +A R+F  +  KN V W+ MI+ + +HGQ +EAL  FY +++ S   P  VTFL +L+AC
Sbjct:   473 EARRLFDLMTKKNEVTWNTMISGYGLHGQGQEALNIFYEMLN-SGITPTPVTFLCVLYAC 531

Query:    63 SYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------ETEP--YV 107
             S++GL++EG ++F+ M+H +  + +++HY   VD+L                  EP   V
Sbjct:   532 SHAGLVKEGDEIFNSMIHRYGFEPSVKHYACMVDILGRAGHLQRALQFIEAMSIEPGSSV 591

Query:   108 WGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
             W  LLGACRIH +  +   V++  F LDP N  Y+  L
Sbjct:   592 WETLLGACRIHKDTNLARTVSEKLFELDPDNVGYHVLL 629

GO:0003674 "molecular_function" evidence=ND

GO:0000963 "mitochondrial RNA processing" evidence=IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0016554 "cytidine to uridine editing" evidence=IMP

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:4515103421 AT4G19191 "AT4G19191" [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 8.9e-22, P = 8.9e-22
 Identities = 63/158 (39%), Positives = 91/158 (57%)

Query:     3 DAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFAC 62
             +A  IF    +K VV W+ MIA +A++G   EAL+ F  +I   D KPN++TFL++L AC
Sbjct:   411 EARDIFDNTPEKTVVTWTTMIAGYALNGIFLEALKLFSKMIDL-DYKPNHITFLAVLQAC 469

Query:    63 SYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT-GETEPY--------------V 107
             ++SG +E+G + F IM   + +   L+HY   VDLL   G+ E                +
Sbjct:   470 AHSGSLEKGWEYFHIMKQVYNISPGLDHYSCMVDLLGRKGKLEEALELIRNMSAKPDAGI 529

Query:   108 WGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
             WGALL AC+IH NVKI E  A+  F+L+P+  A Y  +
Sbjct:   530 WGALLNACKIHRNVKIAEQAAESLFNLEPQMAAPYVEM 567

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 262 (97.3 bits), Expect = 1.0e-21, P = 1.0e-21
 Identities = 59/157 (37%), Positives = 88/157 (56%)

Query:     1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
             M++A  +F  I  K+V  W+ +I+ +A HG  REA+  F + +     KPN +TF ++L 
Sbjct:   298 MEEALEVFKNIKKKSVQAWTALISGYAYHGHGREAISKF-MEMQKMGIKPNVITFTAVLT 356

Query:    61 ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG----ETEPYV--------- 107
             ACSY+GL+EEG  +F  M  D+ L   +EHYG  VDLL       E + ++         
Sbjct:   357 ACSYTGLVEEGKLIFYSMERDYNLKPTIEHYGCIVDLLGRAGLLDEAKRFIQEMPLKPNA 416

Query:   108 --WGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
               WGALL ACRIH N+++GE + +    +DP +   Y
Sbjct:   417 VIWGALLKACRIHKNIELGEEIGEILIAIDPYHGGRY 453

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:2175653 AT5G39350 "AT5G39350" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 1.2e-21, P = 1.2e-21
 Identities = 62/164 (37%), Positives = 89/164 (54%)

Query:     1 MDDAERIFGGIIDKN----VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFL 56
             ++ A +IF GI +K+    VV+W  +I+ + +HG    AL+ F  ++  S   PN +TF 
Sbjct:   471 LESAHKIFNGIQEKHKSKDVVLWGALISGYGMHGDGHNALQVFMEMVR-SGVTPNEITFT 529

Query:    57 SILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGE---------TEPY 106
             S L ACS+SGL+EEG+ +F  M+  ++      HY   VDLL   G          T P+
Sbjct:   530 SALNACSHSGLVEEGLTLFRFMLEHYKTLARSNHYTCIVDLLGRAGRLDEAYNLITTIPF 589

Query:   107 -----VWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
                  VWGALL AC  H NV++GE+ A   F L+P+N   Y  L
Sbjct:   590 EPTSTVWGALLAACVTHENVQLGEMAANKLFELEPENTGNYVLL 633

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2170548 AT5G40410 [Arabidopsis thaliana (taxid:3702)]

 Score = 258 (95.9 bits), Expect = 2.6e-21, P = 2.6e-21
 Identities = 59/160 (36%), Positives = 93/160 (58%)

Query:     1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
             ++D+  +F  I   + + W+ M+A++A HG  R+A++ F L++H     P++VTF  +L 
Sbjct:   286 LEDSSTVFHEITSPDSMAWTAMLAAYATHGFGRDAIKHFELMVHYGIS-PDHVTFTHLLN 344

Query:    61 ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLL--------ATG-----ETEPY- 106
             ACS+SGL+EEG   F+ M   +++D  L+HY   VDLL        A G       EP  
Sbjct:   345 ACSHSGLVEEGKHYFETMSKRYRIDPRLDHYSCMVDLLGRSGLLQDAYGLIKEMPMEPSS 404

Query:   107 -VWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
              VWGALLGACR++ + ++G   A+  F L+P++   Y  L
Sbjct:   405 GVWGALLGACRVYKDTQLGTKAAERLFELEPRDGRNYVML 444

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2082886 EMB2261 "embryo defective 2261" [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 3.1e-21, P = 3.1e-21
 Identities = 61/161 (37%), Positives = 86/161 (53%)

Query:     1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDG-KPNNVTFLSIL 59
             +D A R+F  + ++NV+ W+ MI   A HG     LE F  +I   +G KPN VT+++IL
Sbjct:   525 IDTASRVFNFMENRNVISWTSMITGFAKHGFAIRVLETFNQMIE--EGVKPNEVTYVAIL 582

Query:    60 FACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG----------ETEPY--- 106
              ACS+ GL+ EG + F+ M  D ++   +EHY   VDLL              T P+   
Sbjct:   583 SACSHVGLVSEGWRHFNSMYEDHKIKPKMEHYACMVDLLCRAGLLTDAFEFINTMPFQAD 642

Query:   107 --VWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
               VW   LGACR+H N ++G+L A+    LDP   A Y  L
Sbjct:   643 VLVWRTFLGACRVHSNTELGKLAARKILELDPNEPAAYIQL 683

GO:0009507 "chloroplast" evidence=ISM

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP;NAS

TAIR|locus:2102514 AT3G56550 [Arabidopsis thaliana (taxid:3702)]

 Score = 254 (94.5 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 54/157 (34%), Positives = 88/157 (56%)

Query:     1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
             +++A  +F G+  ++V+ W+ MI  + +HG   EA+  F  ++  S  +PN +TFL +L 
Sbjct:   259 LENAIGVFNGMRKRDVLTWNSMIIGYGVHGHGVEAISFFRKMV-ASGVRPNAITFLGLLL 317

Query:    61 ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA-TGETE--------------P 105
              CS+ GL++EG++ F+IM   F L  N++HYG  VDL    G+ E              P
Sbjct:   318 GCSHQGLVKEGVEHFEIMSSQFHLTPNVKHYGCMVDLYGRAGQLENSLEMIYASSCHEDP 377

Query:   106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY 142
              +W  LLG+C+IH N+++GE+  K    L+  N   Y
Sbjct:   378 VLWRTLLGSCKIHRNLELGEVAMKKLVQLEAFNAGDY 414

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

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	145
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-32
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-26
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-08
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-07
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	0.002

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

 Score =  118 bits (298), Expect = 6e-32
 Identities = 57/148 (38%), Positives = 84/148 (56%), Gaps = 16/148 (10%)

Query: 13  DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGI 72
           +K+VV W+ ++  +  HG+   A+E F  ++  S   P+ VTF+S+L ACS SG++ +G+
Sbjct: 551 EKDVVSWNILLTGYVAHGKGSMAVELFNRMVE-SGVNPDEVTFISLLCACSRSGMVTQGL 609

Query: 73  KVFDIMVHDFQLDLNLEHYGITVDLLA-TGETE--------------PYVWGALLGACRI 117
           + F  M   + +  NL+HY   VDLL   G+                P VWGALL ACRI
Sbjct: 610 EYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRI 669

Query: 118 HHNVKIGELVAKDPFHLDPKNDAYYTSL 145
           H +V++GEL A+  F LDP +  YY  L
Sbjct: 670 HRHVELGELAAQHIFELDPNSVGYYILL 697

Length = 857

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

 Score =  103 bits (259), Expect = 1e-26
 Identities = 53/160 (33%), Positives = 85/160 (53%), Gaps = 16/160 (10%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           M+DA  +F  +  KN++ W+ +IA +  HG+  +A+E F  +I      PN+VTFL++L 
Sbjct: 376 MEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIA-EGVAPNHVTFLAVLS 434

Query: 61  ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLL---------------ATGETEP 105
           AC YSGL E+G ++F  M  + ++     HY   ++LL               A  +   
Sbjct: 435 ACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTV 494

Query: 106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL 145
            +W ALL ACRIH N+++G L A+  + + P+    Y  L
Sbjct: 495 NMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVL 534

Length = 697

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

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDG-KPNNVTFLSIL 59
           ++DA  +F G+ +K  V W+ M+A +A+HG   EAL  +Y +     G   +  TF  ++
Sbjct: 275 IEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEM--RDSGVSIDQFTFSIMI 332

Query: 60  FACSYSGLIE 69
              S   L+E
Sbjct: 333 RIFSRLALLE 342

Length = 697

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

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
           +D A  +F  I +K+V+ W+ +IA   ++ +  EAL   +        KPN+VT ++ L 
Sbjct: 440 IDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEAL--IFFRQMLLTLKPNSVTLIAALS 497

Query: 61  ACSYSGLIEEG 71
           AC+  G +  G
Sbjct: 498 ACARIGALMCG 508

Length = 857

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

 Score = 47.2 bits (112), Expect = 5e-07
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF 60
             +AE++F  +  K+ V W+ MI+ +  +G   +ALE + L+   +   P+ +T  S+L 
Sbjct: 339 WGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNV-SPDEITIASVLS 397

Query: 61  ACSYSGLIEEGIKV 74
           AC+  G ++ G+K+
Sbjct: 398 ACACLGDLDVGVKL 411

Length = 857

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

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 1   MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIH-CSDGKPNNVTFLSIL 59
           + DA R+F  + ++N+  W  +I      G  REA   F  +    SD +P   TF+ +L
Sbjct: 174 LIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPR--TFVVML 231

Query: 60  FACSYSGLIEEG 71
            A +  G    G
Sbjct: 232 RASAGLGSARAG 243

Length = 697

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	145
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.97
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.96
PLN03077	857	Protein ECB2; Provisional	99.96
PLN03077	857	Protein ECB2; Provisional	99.95
PLN03218	1060	maturation of RBCL 1; Provisional	99.95
PLN03218	1060	maturation of RBCL 1; Provisional	99.94
PF13041	50	PPR_2: PPR repeat family	99.75
PF13041	50	PPR_2: PPR repeat family	99.66
PF12854	34	PPR_1: PPR repeat	99.18
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.18
PF12854	34	PPR_1: PPR repeat	99.16
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.06
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.01
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.98
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.95
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.93
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.86
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.79
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.74
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.67
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.67
PRK15359	144	type III secretion system chaperone protein SscB;	98.63
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.62
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.56
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.44
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.42
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.4
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.38
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.36
KOG1126	638	consensus DNA-binding cell division cycle control	98.34
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.3
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.3
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.27
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.27
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.25
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.24
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.23
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.21
PRK11189	296	lipoprotein NlpI; Provisional	98.19
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.18
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.18
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.17
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.15
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	98.15
PRK12370	553	invasion protein regulator; Provisional	98.14
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.08
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.06
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.05
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.04
PRK11189	296	lipoprotein NlpI; Provisional	97.95
KOG1126	638	consensus DNA-binding cell division cycle control	97.91
KOG0553	304	consensus TPR repeat-containing protein [General f	97.89
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.88
PRK12370	553	invasion protein regulator; Provisional	97.87
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.81
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.77
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.77
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.74
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.73
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.68
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.67
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.65
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.61
PRK14574	822	hmsH outer membrane protein; Provisional	97.61
PRK15359	144	type III secretion system chaperone protein SscB;	97.58
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.56
KOG3941	406	consensus Intermediate in Toll signal transduction	97.52
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.52
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.44
KOG1129	478	consensus TPR repeat-containing protein [General f	97.44
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.42
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.4
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.4
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.39
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.37
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.36
PRK14574	822	hmsH outer membrane protein; Provisional	97.34
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.34
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.34
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.32
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.31
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.3
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.3
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.29
KOG2003	840	consensus TPR repeat-containing protein [General f	97.23
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.22
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.21
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.17
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.15
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.14
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.12
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.11
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.06
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.04
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.03
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.99
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.97
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	96.96
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.96
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.94
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	96.9
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	96.88
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.82
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	96.8
PLN02789	320	farnesyltranstransferase	96.78
PRK10803	263	tol-pal system protein YbgF; Provisional	96.71
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.68
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.66
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.66
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.63
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	96.63
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.61
PF13428	44	TPR_14: Tetratricopeptide repeat	96.52
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.44
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.42
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.42
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.4
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	96.35
KOG2076	895	consensus RNA polymerase III transcription factor	96.3
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.3
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.25
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.23
KOG1129	478	consensus TPR repeat-containing protein [General f	96.22
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.19
PF13371	73	TPR_9: Tetratricopeptide repeat	96.18
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.16
PF13371	73	TPR_9: Tetratricopeptide repeat	96.13
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.12
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	96.09
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	95.96
KOG1128	777	consensus Uncharacterized conserved protein, conta	95.91
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	95.88
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	95.81
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.8
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.77
KOG1125	579	consensus TPR repeat-containing protein [General f	95.7
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	95.68
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	95.66
KOG2076	895	consensus RNA polymerase III transcription factor	95.63
KOG4570	418	consensus Uncharacterized conserved protein [Funct	95.62
KOG2003	840	consensus TPR repeat-containing protein [General f	95.61
KOG0547	606	consensus Translocase of outer mitochondrial membr	95.61
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	95.5
KOG3060	289	consensus Uncharacterized conserved protein [Funct	95.49
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.48
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	95.39
PRK14720	906	transcript cleavage factor/unknown domain fusion p	95.39
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	95.34
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.34
KOG1915	677	consensus Cell cycle control protein (crooked neck	95.32
KOG3941	406	consensus Intermediate in Toll signal transduction	95.26
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.24
PF12688	120	TPR_5: Tetratrico peptide repeat	95.23
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	95.2
KOG2047	835	consensus mRNA splicing factor [RNA processing and	95.14
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	95.04
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	94.98
PRK14720	906	transcript cleavage factor/unknown domain fusion p	94.87
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.68
COG3898	531	Uncharacterized membrane-bound protein [Function u	94.62
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	94.52
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	94.5
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	94.46
PLN02789	320	farnesyltranstransferase	94.4
KOG0495	913	consensus HAT repeat protein [RNA processing and m	94.39
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	94.36
PF03704	146	BTAD: Bacterial transcriptional activator domain;	94.18
KOG3785	557	consensus Uncharacterized conserved protein [Funct	94.09
KOG1128	777	consensus Uncharacterized conserved protein, conta	93.99
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	93.95
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.92
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	93.77
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	93.62
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	93.58
KOG2047	835	consensus mRNA splicing factor [RNA processing and	93.58
KOG1125	579	consensus TPR repeat-containing protein [General f	93.57
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	93.52
PRK15331	165	chaperone protein SicA; Provisional	93.5
KOG0553	304	consensus TPR repeat-containing protein [General f	93.41
KOG2796	366	consensus Uncharacterized conserved protein [Funct	93.38
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	93.09
PF13428	44	TPR_14: Tetratricopeptide repeat	93.05
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.95
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.87
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	92.81
PF13512	142	TPR_18: Tetratricopeptide repeat	92.77
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	92.74
KOG4340	459	consensus Uncharacterized conserved protein [Funct	92.73
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	92.72
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	92.63
PRK10803	263	tol-pal system protein YbgF; Provisional	92.44
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	92.43
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	92.15
PF13431	34	TPR_17: Tetratricopeptide repeat	91.96
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	91.96
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	91.87
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	91.69
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	91.5
smart00299	140	CLH Clathrin heavy chain repeat homology.	91.48
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	91.23
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	91.07
KOG0495	913	consensus HAT repeat protein [RNA processing and m	91.03
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.92
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	90.81
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	90.69
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	90.08
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	90.04
PF13762	145	MNE1: Mitochondrial splicing apparatus component	89.74
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	89.65
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	89.63
KOG3616	1636	consensus Selective LIM binding factor [Transcript	89.55
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	89.38
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	89.07
PF13512	142	TPR_18: Tetratricopeptide repeat	88.95
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	88.59
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	88.15
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	87.87
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	87.75
PRK10564	303	maltose regulon periplasmic protein; Provisional	87.71
COG3898	531	Uncharacterized membrane-bound protein [Function u	87.53
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	87.51
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	87.46
PF13929	292	mRNA_stabil: mRNA stabilisation	87.45
COG3629	280	DnrI DNA-binding transcriptional activator of the	87.41
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	87.33
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	87.24
PF14853	53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	86.85
COG4700	251	Uncharacterized protein conserved in bacteria cont	86.83
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	86.63
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	86.39
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	86.35
PRK15331	165	chaperone protein SicA; Provisional	86.34
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	86.28
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	85.85
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	85.8
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	85.16
KOG3785	557	consensus Uncharacterized conserved protein [Funct	84.3
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	84.26
KOG4648	536	consensus Uncharacterized conserved protein, conta	84.17
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	83.77
COG4105	254	ComL DNA uptake lipoprotein [General function pred	83.42
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	83.4
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	83.26
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	83.19
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	83.09
KOG2376	652	consensus Signal recognition particle, subunit Srp	82.83
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	82.76
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	82.76
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	82.65
PF13762	145	MNE1: Mitochondrial splicing apparatus component	82.28
KOG2376	652	consensus Signal recognition particle, subunit Srp	80.93
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	80.55

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

Probab=99.97  E-value=4.3e-30  Score=204.62  Aligned_cols=144  Identities=36%  Similarity=0.683  Sum_probs=137.6

Q ss_pred             CchHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113            1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus         1 ~~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      +++|.++|++|.+||+++||+||.+|+++|+.++|.++|++|.+ .|++||..||+++|.+|++.|.+++|.++|+.|..
T Consensus       376 ~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~-~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~  454 (697)
T PLN03081        376 MEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIA-EGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSE  454 (697)
T ss_pred             HHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999 99999999999999999999999999999999986


Q ss_pred             hcCcCccHHHHHHHHHHHhcC---------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCcccC
Q 047113           81 DFQLDLNLEHYGITVDLLATG---------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL  145 (145)
Q Consensus        81 ~~~~~~~~~~~~~li~~~~~~---------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~l  145 (145)
                      +.|+.|+..+|+++|++|++.               .|+..+|++|+.+|+..|+++.|..+++++.+++|++...|++|
T Consensus       455 ~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L  534 (697)
T PLN03081        455 NHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVL  534 (697)
T ss_pred             hcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHH
Confidence            789999999999999999998               78999999999999999999999999999999999888777653

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

Probab=99.96  E-value=3.7e-30  Score=205.02  Aligned_cols=138  Identities=22%  Similarity=0.332  Sum_probs=129.9

Q ss_pred             CchHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113            1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus         1 ~~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      +++|.++|++|+++|+++||+||.+|+++|++++|+++|++|.+ .|++||..||++++.+|++.|.++.|.+++..|. 
T Consensus       275 ~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~-~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~-  352 (697)
T PLN03081        275 IEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRD-SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLI-  352 (697)
T ss_pred             HHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHH-
Confidence            47899999999999999999999999999999999999999999 9999999999999999999999999999999999 


Q ss_pred             hcCcCccHHHHHHHHHHHhcC--------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC--CCCCCCC
Q 047113           81 DFQLDLNLEHYGITVDLLATG--------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH--LDPKNDA  140 (145)
Q Consensus        81 ~~~~~~~~~~~~~li~~~~~~--------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~~~  140 (145)
                      +.|+.||..+|++||++|+++              .||..+||+||.+|++.|+.++|.++|++|.+  +.|+..+
T Consensus       353 ~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T  428 (697)
T PLN03081        353 RTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVT  428 (697)
T ss_pred             HhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHH
Confidence            899999999999999999998              78999999999999999999999999999887  5565433

>PLN03077 Protein ECB2; Provisional

Probab=99.96  E-value=2.5e-28  Score=198.18  Aligned_cols=143  Identities=41%  Similarity=0.756  Sum_probs=137.3

Q ss_pred             CchHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113            1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus         1 ~~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      +++|.++|+.+ .||+++||+||.+|+++|+.++|+++|++|.+ .|++||..||+.+|.+|++.|.+++|.++|+.|..
T Consensus       540 ~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~-~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~  617 (857)
T PLN03077        540 MNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVE-SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEE  617 (857)
T ss_pred             HHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHH-cCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHH
Confidence            36899999999 89999999999999999999999999999999 99999999999999999999999999999999997


Q ss_pred             hcCcCccHHHHHHHHHHHhcC---------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCcccC
Q 047113           81 DFQLDLNLEHYGITVDLLATG---------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYTSL  145 (145)
Q Consensus        81 ~~~~~~~~~~~~~li~~~~~~---------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~l  145 (145)
                      +.|+.|+..+|++++++|++.               .||..+|++|+.+|..+|+.+.++...+++.+++|+++.+|++|
T Consensus       618 ~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l~p~~~~~y~ll  697 (857)
T PLN03077        618 KYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILL  697 (857)
T ss_pred             HhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhhCCCCcchHHHH
Confidence            799999999999999999999               89999999999999999999999999999999999999888764

>PLN03077 Protein ECB2; Provisional

Probab=99.95  E-value=2.5e-28  Score=198.23  Aligned_cols=139  Identities=15%  Similarity=0.236  Sum_probs=131.9

Q ss_pred             CchHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113            1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus         1 ~~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      +++|.++|++|+.||+++||+||.+|++.|++++|+++|++|.. .|++||..||+.+|.+|++.|+++.|.+++..|. 
T Consensus       238 ~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~-~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~-  315 (857)
T PLN03077        238 VVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRE-LSVDPDLMTITSVISACELLGDERLGREMHGYVV-  315 (857)
T ss_pred             HHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHH-
Confidence            36899999999999999999999999999999999999999999 9999999999999999999999999999999999 


Q ss_pred             hcCcCccHHHHHHHHHHHhcC--------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC--CCCCCCCC
Q 047113           81 DFQLDLNLEHYGITVDLLATG--------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH--LDPKNDAY  141 (145)
Q Consensus        81 ~~~~~~~~~~~~~li~~~~~~--------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~  141 (145)
                      +.|+.||..+||+||++|+++              .||..+||++|.+|++.|++++|.++|++|.+  +.|+..++
T Consensus       316 ~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~  392 (857)
T PLN03077        316 KTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITI  392 (857)
T ss_pred             HhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeH
Confidence            999999999999999999998              88999999999999999999999999999976  56755443

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.95  E-value=1.3e-27  Score=195.50  Aligned_cols=135  Identities=15%  Similarity=0.159  Sum_probs=96.5

Q ss_pred             chHHHHhccCCC----CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID----KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~----~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.++|++|.+    |+..+||+||.+|++.|++++|.++|++|.+ .|+.||..+|+++|++|++.|+++.|.++|+.
T Consensus       596 deA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~-~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~e  674 (1060)
T PLN03218        596 DRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK-KGVKPDEVFFSALVDVAGHAGDLDKAFEILQD  674 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            456666666653    4556777777777777777777777777776 77777777777777777777777777777777


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC--CCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH--LDPK  137 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~  137 (145)
                      |. +.|+.||..+|++||++|+++                  .||..+||+||.+|++.|++++|.++|++|.+  +.|+
T Consensus       675 M~-k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd  753 (1060)
T PLN03218        675 AR-KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPN  753 (1060)
T ss_pred             HH-HcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            76 667777777777777777766                  67777888888888888888888888887765  4454


Q ss_pred             C
Q 047113          138 N  138 (145)
Q Consensus       138 ~  138 (145)
                      .
T Consensus       754 ~  754 (1060)
T PLN03218        754 T  754 (1060)
T ss_pred             H
Confidence            3

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.94  E-value=4.4e-27  Score=192.40  Aligned_cols=129  Identities=21%  Similarity=0.273  Sum_probs=88.8

Q ss_pred             chHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhh
Q 047113            2 DDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus         2 ~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      ++|.++|+.|+.||..+||.||.+|++.|++++|.++|++|.+ .|+.||..+||++|++|++.|+++.|.++|++|. +
T Consensus       423 ~eAl~lf~~M~~pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~-~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~-~  500 (1060)
T PLN03218        423 KEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQE-AGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMV-N  500 (1060)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHH-H
Confidence            3566666666666667777777777777777777777777766 6777777777777777777777777777777776 6


Q ss_pred             cCcCccHHHHHHHHHHHhcC------------------CCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           82 FQLDLNLEHYGITVDLLATG------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        82 ~~~~~~~~~~~~li~~~~~~------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      .|+.||..||++||++|++.                  .||..+||+||.+|++.|++++|.++|++|.
T Consensus       501 ~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~  569 (1060)
T PLN03218        501 AGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMK  569 (1060)
T ss_pred             cCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            66677777777777777666                  5666666666666666666666666666664

>PF13041 PPR_2: PPR repeat family

Probab=99.75  E-value=4.6e-18  Score=92.01  Aligned_cols=50  Identities=22%  Similarity=0.286  Sum_probs=46.4

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY   64 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~   64 (145)
                      ||+++||+||++|+++|++++|.++|++|.+ .|++||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~-~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKK-RGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHcC
Confidence            7899999999999999999999999999998 9999999999999999875

>PF13041 PPR_2: PPR repeat family

Probab=99.66  E-value=3.3e-16  Score=84.68  Aligned_cols=50  Identities=24%  Similarity=0.389  Sum_probs=48.7

Q ss_pred             CcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhc
Q 047113           50 PNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        50 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  100 (145)
                      ||..+||++|++|++.|++++|.++|++|. +.|+.||..||++||++|+|
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~-~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMK-KRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHH-HcCCCCCHHHHHHHHHHHcC
Confidence            899999999999999999999999999999 99999999999999999986

>PF12854 PPR_1: PPR repeat

Probab=99.18  E-value=3.3e-11  Score=59.57  Aligned_cols=32  Identities=25%  Similarity=0.503  Sum_probs=16.6

Q ss_pred             CCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113           47 DGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus        47 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      |++||..|||++|+++|+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            44555555555555555555555555555544

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.18  E-value=2.7e-10  Score=85.03  Aligned_cols=113  Identities=14%  Similarity=0.221  Sum_probs=90.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHH----HHHHHHHHhhhhcCcCccHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIE----EGIKVFDIMVHDFQLDLNLEH   90 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~----~a~~~~~~m~~~~~~~~~~~~   90 (145)
                      +..+||.+|.+-+-.    ...++..+|.. ..++||..|||+++++.++.|+++    .+.+++.+|+ .-|++|+..+
T Consensus       241 ~~~aFN~lI~~~S~~----~~K~Lv~EMis-qkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmK-eiGVePsLsS  314 (625)
T KOG4422|consen  241 YREAFNGLIGASSYS----VGKKLVAEMIS-QKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMK-EIGVEPSLSS  314 (625)
T ss_pred             eHHhhhhhhhHHHhh----ccHHHHHHHHH-hhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHH-HhCCCcchhh
Confidence            344555555444322    22566677788 889999999999999999999876    4678888998 8999999999


Q ss_pred             HHHHHHHHhcC---------------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           91 YGITVDLLATG---------------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        91 ~~~li~~~~~~---------------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      |..+|..+++.                           +.|...|-+.|+.|.+..+.+-|.++..-++.
T Consensus       315 yh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~t  384 (625)
T KOG4422|consen  315 YHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKT  384 (625)
T ss_pred             HHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Confidence            99999999887                           44667899999999999999999988776553

>PF12854 PPR_1: PPR repeat

Probab=99.16  E-value=5.1e-11  Score=58.88  Aligned_cols=31  Identities=26%  Similarity=0.366  Sum_probs=29.7

Q ss_pred             CCchhhHHHHHHHHHHcCChHHHHHHHHHhH
Q 047113           13 DKNVVIWSGMIASHAIHGQEREALEAFYLVI   43 (145)
Q Consensus        13 ~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~   43 (145)
                      +||.+|||+||++||+.|++++|.++|++|+
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            5899999999999999999999999999994

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.06  E-value=2.9e-10  Score=56.14  Aligned_cols=35  Identities=26%  Similarity=0.376  Sum_probs=32.0

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN   52 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~   52 (145)
                      ++||+||.+|++.|++++|.++|++|.+ .|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~-~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLE-RGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHH-cCCCCCC
Confidence            4799999999999999999999999999 9999984

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.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.01  E-value=2.5e-09  Score=80.03  Aligned_cols=77  Identities=10%  Similarity=0.085  Sum_probs=35.3

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.++|+++..   ++..+++.++..+.+.|++++|.+.|+.+.. .+-.+.    ...+..+...+.+.|++++|...
T Consensus       124 ~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~  202 (389)
T PRK11788        124 DRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEK-LGGDSLRVEIAHFYCELAQQALARGDLDAARAL  202 (389)
T ss_pred             HHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHH-hcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            345555554432   2344555555555555555555555555544 221111    11223344444445555555555


Q ss_pred             HHHhh
Q 047113           75 FDIMV   79 (145)
Q Consensus        75 ~~~m~   79 (145)
                      ++++.
T Consensus       203 ~~~al  207 (389)
T PRK11788        203 LKKAL  207 (389)
T ss_pred             HHHHH
Confidence            55544

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.98  E-value=1.1e-09  Score=53.91  Aligned_cols=34  Identities=24%  Similarity=0.328  Sum_probs=30.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP   50 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p   50 (145)
                      +++||++|.+|++.|++++|.++|++|++ .|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~-~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKE-QGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHH-hCCCC
Confidence            36899999999999999999999999998 89887

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.95  E-value=6.2e-09  Score=77.95  Aligned_cols=128  Identities=15%  Similarity=0.043  Sum_probs=73.4

Q ss_pred             chHHHHhccCCC--C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGIID--K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+++.+  | +...|..+...+.+.|++++|...|+++.. .+-.....+++.+..++.+.|+++.|...++.+
T Consensus       197 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~-~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  275 (389)
T PRK11788        197 DAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEE-QDPEYLSEVLPKLMECYQALGDEAEGLEFLRRA  275 (389)
T ss_pred             HHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            345555555432  2 344566666666666666666666666654 221112345566666666666666666666666


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC----------------CCchhhHHHHHHHHHh---ccChhHHHHHHccCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG----------------ETEPYVWGALLGACRI---HHNVKIGELVAKDPFH  133 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~----------------~p~~~~~~~li~~~~~---~g~~~~a~~~~~~~~~  133 (145)
                      . .  ..|+...+..++..|.+.                .|+..+++.++..+..   .|+.+++..+++++.+
T Consensus       276 ~-~--~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~  346 (389)
T PRK11788        276 L-E--EYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVG  346 (389)
T ss_pred             H-H--hCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHH
Confidence            6 2  234544555566655554                5666666666666553   3466666666666554

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.93  E-value=1.6e-08  Score=75.77  Aligned_cols=110  Identities=19%  Similarity=0.127  Sum_probs=94.4

Q ss_pred             hccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc
Q 047113            8 FGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN   87 (145)
Q Consensus         8 f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~   87 (145)
                      +-+..++...||.+||.+.|+--..+.|.+++++-+. ...+.+..+||.+|.+-+-.    .+..+..+|. ...+.||
T Consensus       199 ~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~-~k~kv~~~aFN~lI~~~S~~----~~K~Lv~EMi-sqkm~Pn  272 (625)
T KOG4422|consen  199 LFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRA-AKGKVYREAFNGLIGASSYS----VGKKLVAEMI-SQKMTPN  272 (625)
T ss_pred             HHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHH-hhheeeHHhhhhhhhHHHhh----ccHHHHHHHH-HhhcCCc
Confidence            3344445668999999999999999999999999998 88899999999999876644    3478889999 7889999


Q ss_pred             HHHHHHHHHHHhcC----------------------CCchhhHHHHHHHHHhccChhH
Q 047113           88 LEHYGITVDLLATG----------------------ETEPYVWGALLGACRIHHNVKI  123 (145)
Q Consensus        88 ~~~~~~li~~~~~~----------------------~p~~~~~~~li~~~~~~g~~~~  123 (145)
                      ..|+|+++++.++-                      .|...+|..+|.-+++.++..+
T Consensus       273 l~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  273 LFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             hHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh
Confidence            99999999988876                      8899999999999999888744

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

Probab=98.86  E-value=3.8e-08  Score=79.66  Aligned_cols=133  Identities=8%  Similarity=-0.063  Sum_probs=78.9

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +|.+.|+.+.   +.+..+|..+...+...|++++|..+++.+.. .. +.+...+..+...+...|+++.|...++.+.
T Consensus       653 ~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~  730 (899)
T TIGR02917       653 KAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQK-QH-PKAALGFELEGDLYLRQKDYPAAIQAYRKAL  730 (899)
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-hC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4455554432   22445566666666666666666666666654 32 3345556666666666666666666666665


Q ss_pred             hhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           80 HDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                       .  ..|+..++..+..+|.+.                 +.+..+++.+...|...|+.++|...++++.+..|+++.
T Consensus       731 -~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~  805 (899)
T TIGR02917       731 -K--RAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAV  805 (899)
T ss_pred             -h--hCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHH
Confidence             2  234435555555555544                 445566777777777777777777777777776665543

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.

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

Probab=98.79  E-value=8.1e-09  Score=49.54  Aligned_cols=31  Identities=29%  Similarity=0.295  Sum_probs=26.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCC
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDG   48 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~   48 (145)
                      ++||+||++|++.|++++|.++|++|.+ .|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~-~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRE-RGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhH-CcC
Confidence            4788899999999999999999988887 664

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.

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

Probab=98.74  E-value=1.3e-07  Score=76.59  Aligned_cols=32  Identities=13%  Similarity=-0.025  Sum_probs=15.5

Q ss_pred             hhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113          105 PYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       105 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      ..+|..+...+...|++++|..+++.+.+..|
T Consensus       669 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  700 (899)
T TIGR02917       669 TEAQIGLAQLLLAAKRTESAKKIAKSLQKQHP  700 (899)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc
Confidence            34444444555555555555555554444444

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.

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

Probab=98.67  E-value=1.1e-07  Score=68.62  Aligned_cols=137  Identities=14%  Similarity=0.120  Sum_probs=87.6

Q ss_pred             chHHHHhccC--CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            2 DDAERIFGGI--IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         2 ~~A~~~f~~m--~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ++|.++++..  +.++...+..++..+.+.|+++++..+++........+++...|..+-..+.+.|+.+.|...+++..
T Consensus        94 ~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al  173 (280)
T PF13429_consen   94 EEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKAL  173 (280)
T ss_dssp             ------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3555555544  23566778889999999999999999999976523455678888888899999999999999999998


Q ss_pred             hhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           80 HDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        80 ~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                         ...| |....+.++..+...                 +.|...|..+-.+|...|+.++|+..+++..+..|+++..
T Consensus       174 ---~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~  250 (280)
T PF13429_consen  174 ---ELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLW  250 (280)
T ss_dssp             ---HH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHH
T ss_pred             ---HcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccccccccccc
Confidence               3456 477777888777755                 4566778889999999999999999999988888877643

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.67  E-value=2.7e-08  Score=48.83  Aligned_cols=35  Identities=20%  Similarity=0.442  Sum_probs=32.7

Q ss_pred             HHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccH
Q 047113           53 VTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNL   88 (145)
Q Consensus        53 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~   88 (145)
                      .+||++|++|++.|++++|.++|++|. +.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~-~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEML-ERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHH-HcCCCCCC
Confidence            379999999999999999999999999 88999973

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.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.63  E-value=4.3e-07  Score=59.48  Aligned_cols=115  Identities=8%  Similarity=0.031  Sum_probs=93.3

Q ss_pred             HhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcC
Q 047113            7 IFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLD   85 (145)
Q Consensus         7 ~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~   85 (145)
                      +|+...+-++..+..+-.++.+.|++++|...|+....   +.| +...|..+-.++...|+++.|...|+... .  ..
T Consensus        15 ~~~~al~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al-~--l~   88 (144)
T PRK15359         15 ILKQLLSVDPETVYASGYASWQEGDYSRAVIDFSWLVM---AQPWSWRAHIALAGTWMMLKEYTTAINFYGHAL-M--LD   88 (144)
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHH-h--cC
Confidence            33333333444566778889999999999999999865   345 77889999999999999999999999998 3  34


Q ss_pred             ccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCcc
Q 047113           86 LNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYT  143 (145)
Q Consensus        86 ~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  143 (145)
                      |+                +...+..+-.++...|++++|...+++..+..|+++.++.
T Consensus        89 p~----------------~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~~  130 (144)
T PRK15359         89 AS----------------HPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADASWSE  130 (144)
T ss_pred             CC----------------CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHH
Confidence            43                6677888888999999999999999999999998876653

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.62  E-value=5.3e-08  Score=47.66  Aligned_cols=33  Identities=24%  Similarity=0.418  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc
Q 047113           53 VTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL   86 (145)
Q Consensus        53 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~   86 (145)
                      .|||++|.+|++.|+++.|.++|+.|. +.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~-~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMK-EQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHH-HhCCCC
Confidence            589999999999999999999999999 889987

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.56  E-value=3.8e-06  Score=57.59  Aligned_cols=135  Identities=9%  Similarity=-0.003  Sum_probs=95.7

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|++..   +.+...|..+...+...|++++|...|++..+ .. +.+...+..+...+...|++++|...++..
T Consensus        48 ~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~  125 (234)
T TIGR02521        48 EVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALT-LN-PNNGDVLNNYGTFLCQQGKYEQAMQQFEQA  125 (234)
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-hC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            45666666542   23566788888899999999999999988765 32 235567777888888999999999999988


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      ............+..+..+|.+.                 +.+...+..+...+...|++++|...+++..+..|++
T Consensus       126 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~  202 (234)
T TIGR02521       126 IEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQT  202 (234)
T ss_pred             HhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence            73212222344555555555544                 3345678888888899999999999988877665543

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.

>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=98.44  E-value=4.3e-06  Score=57.82  Aligned_cols=95  Identities=11%  Similarity=0.070  Sum_probs=82.6

Q ss_pred             HHHhccC--CCCchhhHHHHHHHHHHc-----CChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc-----------
Q 047113            5 ERIFGGI--IDKNVVIWSGMIASHAIH-----GQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSG-----------   66 (145)
Q Consensus         5 ~~~f~~m--~~~~~~~~~~li~a~~~~-----g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~-----------   66 (145)
                      ...|+..  ..+|-.+|..+|..+.+.     |..+=....++.|.+ .|+.-|..+|+.||+.+=+..           
T Consensus        34 ~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~e-fgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F  112 (228)
T PF06239_consen   34 EELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDE-FGVEKDLEVYKALLDVFPKGKFVPRNFFQAEF  112 (228)
T ss_pred             HHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHH-cCCcccHHHHHHHHHhCCCCCcccccHHHHHh
Confidence            4566665  567889999999999864     778888999999999 999999999999999987632           


Q ss_pred             -----hHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC
Q 047113           67 -----LIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        67 -----~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                           +-+-|..++++|. +.|+.||..|+..|++.+++.
T Consensus       113 ~hyp~Qq~c~i~lL~qME-~~gV~Pd~Et~~~ll~iFG~~  151 (228)
T PF06239_consen  113 MHYPRQQECAIDLLEQME-NNGVMPDKETEQMLLNIFGRK  151 (228)
T ss_pred             ccCcHHHHHHHHHHHHHH-HcCCCCcHHHHHHHHHHhccc
Confidence                 3367999999999 999999999999999999988

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

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

Probab=98.42  E-value=3e-07  Score=43.86  Aligned_cols=31  Identities=32%  Similarity=0.467  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhhccchHHHHHHHHHHhhhhcCc
Q 047113           53 VTFLSILFACSYSGLIEEGIKVFDIMVHDFQL   84 (145)
Q Consensus        53 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~   84 (145)
                      +|||++|++|++.|++++|.++|++|. +.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~-~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMR-ERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHh-HCcC
Confidence            489999999999999999999999999 7664

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.

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

Probab=98.40  E-value=2e-05  Score=62.95  Aligned_cols=130  Identities=12%  Similarity=-0.020  Sum_probs=78.7

Q ss_pred             hHHHHhccCC--CC-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            3 DAERIFGGII--DK-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         3 ~A~~~f~~m~--~~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      +|...|+...  .| +..+|..+...+...|++++|...|+.... .  .| +...|..+-..+...|+++.|...|+..
T Consensus       349 eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~-~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~ka  425 (615)
T TIGR00990       349 EALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALK-L--NSEDPDIYYHRAQLHFIKGEFAQAGKDYQKS  425 (615)
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-h--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4455555332  12 344566666666667777777777766544 2  23 4556666666667777777777777666


Q ss_pred             hhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           79 VHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      . .  +.| +...+..+..++.+.                 +.+...|+.+-..+...|++++|...|++..++.|..
T Consensus       426 l-~--l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~  500 (615)
T TIGR00990       426 I-D--LDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKET  500 (615)
T ss_pred             H-H--cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCcc
Confidence            6 2  233 344444444444433                 3345677777777778888888888887777766643

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

Probab=98.38  E-value=1.2e-05  Score=50.13  Aligned_cols=82  Identities=15%  Similarity=0.081  Sum_probs=71.1

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCC-CCcHHHHHHHHHHhhccch--------HHHHHHHHHHhhhhcCcCcc
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDG-KPNNVTFLSILFACSYSGL--------IEEGIKVFDIMVHDFQLDLN   87 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~-~p~~~~~~~ll~~~~~~~~--------~~~a~~~~~~m~~~~~~~~~   87 (145)
                      .|-...|..|...+++.....+|+.+++ .|+ .|+..+|+.++.+-++...        .-....+++.|. ..++.|+
T Consensus        26 ~t~i~~I~~~~~~~d~N~I~~lYqslkR-N~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL-~~~lKP~  103 (120)
T PF08579_consen   26 ETQIDNINSCFENEDYNIINPLYQSLKR-NGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDIL-SNKLKPN  103 (120)
T ss_pred             HHHHHHHHHHHhhcchHHHHHHHHHHHh-cCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHH-HhccCCc
Confidence            3556788889999999999999999999 999 9999999999999887542        346788999999 8899999


Q ss_pred             HHHHHHHHHHHhc
Q 047113           88 LEHYGITVDLLAT  100 (145)
Q Consensus        88 ~~~~~~li~~~~~  100 (145)
                      ..||+.++..+.+
T Consensus       104 ~etYnivl~~Llk  116 (120)
T PF08579_consen  104 DETYNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999977654

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 [, , ].

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

Probab=98.36  E-value=5e-06  Score=66.30  Aligned_cols=135  Identities=13%  Similarity=0.083  Sum_probs=107.8

Q ss_pred             chHHHHhccCCC-----C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID-----K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~-----~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.+.|+....     | +...|+.+...+...|++++|+..|+...+   +.|+ ...|..+...+...|+++.|...
T Consensus       311 ~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~---l~P~~~~~~~~la~~~~~~g~~~eA~~~  387 (615)
T TIGR00990       311 EEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIE---LDPRVTQSYIKRASMNLELGDPDKAEED  387 (615)
T ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence            456677775432     2 456789999999999999999999999765   3564 66888888899999999999999


Q ss_pred             HHHhhhhcCcCc-cHHHHHHHHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           75 FDIMVHDFQLDL-NLEHYGITVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        75 ~~~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      |+... +.  .| +...|..+...|...                .| +...|..+...+.+.|++++|+..+++..+..|
T Consensus       388 ~~~al-~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P  464 (615)
T TIGR00990       388 FDKAL-KL--NSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFP  464 (615)
T ss_pred             HHHHH-Hh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            99988 32  34 577888888777765                44 567888888999999999999999999888888


Q ss_pred             CCCCCc
Q 047113          137 KNDAYY  142 (145)
Q Consensus       137 ~~~~~~  142 (145)
                      +++..+
T Consensus       465 ~~~~~~  470 (615)
T TIGR00990       465 EAPDVY  470 (615)
T ss_pred             CChHHH
Confidence            776544

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

Probab=98.34  E-value=2.6e-06  Score=66.66  Aligned_cols=117  Identities=13%  Similarity=0.187  Sum_probs=96.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      ...+|.++-+.|+-.++++.|+++|++..+   +.| ...+|+.+-+-......+|.|...|+...     ..|..+||+
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQ---ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al-----~~~~rhYnA  491 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQ---LDPRFAYAYTLLGHESIATEEFDKAMKSFRKAL-----GVDPRHYNA  491 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhc---cCCccchhhhhcCChhhhhHHHHhHHHHHHhhh-----cCCchhhHH
Confidence            457899999999999999999999999866   556 78899999999999999999999998887     445555554


Q ss_pred             ---HHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           94 ---TVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        94 ---li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                         |.-.|.|.                 +.+.+....+...+-+.|+.|+|++++++...++|.++
T Consensus       492 wYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~  557 (638)
T KOG1126|consen  492 WYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNP  557 (638)
T ss_pred             HHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCc
Confidence               45566666                 55677777788888888888889888888888888765

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.30  E-value=9.4e-06  Score=67.80  Aligned_cols=30  Identities=7%  Similarity=-0.154  Sum_probs=12.4

Q ss_pred             hHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113          107 VWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .+..+-.++...|++++|+..+++..+..|
T Consensus       679 a~~nLA~al~~lGd~~eA~~~l~~Al~l~P  708 (987)
T PRK09782        679 LIRQLAYVNQRLDDMAATQHYARLVIDDID  708 (987)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            333444444444444444444444444333

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

Probab=98.30  E-value=6.1e-06  Score=62.62  Aligned_cols=129  Identities=12%  Similarity=0.137  Sum_probs=105.6

Q ss_pred             CchHHHHhccCCCC------chhhHHHHH-------------------------------HHHHHcCChHHHHHHHHHhH
Q 047113            1 MDDAERIFGGIIDK------NVVIWSGMI-------------------------------ASHAIHGQEREALEAFYLVI   43 (145)
Q Consensus         1 ~~~A~~~f~~m~~~------~~~~~~~li-------------------------------~a~~~~g~~~~A~~~~~~m~   43 (145)
                      +|+|+.+|+++.+.      |..+|+.++                               +-|+-.+++++|...|++..
T Consensus       278 fD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRAL  357 (559)
T KOG1155|consen  278 FDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRAL  357 (559)
T ss_pred             HHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHH
Confidence            47899999988642      445555444                               45556778999999999976


Q ss_pred             hhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCc
Q 047113           44 HCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG-----------------ETE  104 (145)
Q Consensus        44 ~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~  104 (145)
                      +   +-| ....|+.+-+-|....+...|.+-++...   .+.| |-..|-.|.++|.-.                 +.|
T Consensus       358 k---LNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAv---di~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnD  431 (559)
T KOG1155|consen  358 K---LNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAV---DINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPND  431 (559)
T ss_pred             h---cCcchhHHHHHhhHHHHHhcccHHHHHHHHHHH---hcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCc
Confidence            5   445 46689999999999999999999999998   3555 899999999999876                 558


Q ss_pred             hhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113          105 PYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus       105 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      ...|.+|-+.|.+.++.++|...|.+.....
T Consensus       432 sRlw~aLG~CY~kl~~~~eAiKCykrai~~~  462 (559)
T KOG1155|consen  432 SRLWVALGECYEKLNRLEEAIKCYKRAILLG  462 (559)
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHhcc
Confidence            8999999999999999999999999876643

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

Probab=98.27  E-value=1.4e-06  Score=70.28  Aligned_cols=121  Identities=16%  Similarity=0.076  Sum_probs=85.6

Q ss_pred             CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC------------------------CCCcHHHHHHHHHHhhccchH
Q 047113           13 DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSD------------------------GKPNNVTFLSILFACSYSGLI   68 (145)
Q Consensus        13 ~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~------------------------~~p~~~~~~~ll~~~~~~~~~   68 (145)
                      .||-+||..+|.-||..|+.+.|- +|..|+. ..                        -.|...||+.++.+|.+.|++
T Consensus        22 ~PnRvtyqsLiarYc~~gdieaat-if~fm~~-ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll~ayr~hGDl   99 (1088)
T KOG4318|consen   22 LPNRVTYQSLIARYCTKGDIEAAT-IFPFMEI-KSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLLKAYRIHGDL   99 (1088)
T ss_pred             CCchhhHHHHHHHHcccCCCcccc-chhhhhc-ccccccchhHHHHHhcccccccccCCCCCchhHHHHHHHHHHhccch
Confidence            378899999999999999999999 8887733 21                        346677888888888888876


Q ss_pred             HH---HHHHHHHhhh---hcC-----------------cCccH----------HHHHHHHHHHhcC--------------
Q 047113           69 EE---GIKVFDIMVH---DFQ-----------------LDLNL----------EHYGITVDLLATG--------------  101 (145)
Q Consensus        69 ~~---a~~~~~~m~~---~~~-----------------~~~~~----------~~~~~li~~~~~~--------------  101 (145)
                      ..   .++.+..+..   ..|                 +-||.          ..|..+++...++              
T Consensus       100 i~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa~~~p~~vfLr  179 (1088)
T KOG4318|consen  100 ILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLR  179 (1088)
T ss_pred             HHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCcccccchHHHHHH
Confidence            43   2221111110   111                 12332          2355555555444              


Q ss_pred             ---------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113          102 ---------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus       102 ---------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                                           .|+..++..++++-...|+++-|..+..+|++-.
T Consensus       180 qnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~g  234 (1088)
T KOG4318|consen  180 QNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKG  234 (1088)
T ss_pred             HhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcC
Confidence                                 5899999999999999999999999999999843

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.27  E-value=4.9e-05  Score=52.02  Aligned_cols=130  Identities=12%  Similarity=0.051  Sum_probs=96.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|++..   +.+...+..+...+...|++++|...|++... ....| ....+..+-..+...|+++.|...+..
T Consensus        82 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  160 (234)
T TIGR02521        82 EKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIE-DPLYPQPARSLENAGLCALKAGDFDKAEKYLTR  160 (234)
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHh-ccccccchHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            45677776443   34567888899999999999999999999876 43223 455677778888999999999999999


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      .. ... ..+...+..+...+.+.                 +.+...+..+...+...|+.++|..+.+.+.+.
T Consensus       161 ~~-~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       161 AL-QID-PQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HH-HhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            88 322 22455666676666655                 335567778888889999999999988776543

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.25  E-value=1.6e-05  Score=63.95  Aligned_cols=24  Identities=13%  Similarity=0.139  Sum_probs=10.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYL   41 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~   41 (145)
                      .|..+..++.+.|++++|...++.
T Consensus       146 a~~~la~~l~~~g~~~eA~~~~~~  169 (656)
T PRK15174        146 IFALHLRTLVLMDKELQAISLART  169 (656)
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHH
Confidence            344444444444444444444443

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.24  E-value=1.5e-05  Score=64.18  Aligned_cols=112  Identities=14%  Similarity=0.051  Sum_probs=55.1

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHH----HHHHHHHhhhhcCcCc-cHHHHHHHHH
Q 047113           22 MIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEE----GIKVFDIMVHDFQLDL-NLEHYGITVD   96 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~----a~~~~~~m~~~~~~~~-~~~~~~~li~   96 (145)
                      +..++.+.|++++|...|+.... .. +-+...+..+-..+.+.|++++    |...++... .  ..| +...+..+..
T Consensus       218 l~~~l~~~g~~~eA~~~~~~al~-~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al-~--l~P~~~~a~~~lg~  292 (656)
T PRK15174        218 AVDTLCAVGKYQEAIQTGESALA-RG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHAL-Q--FNSDNVRIVTLYAD  292 (656)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHH-h--hCCCCHHHHHHHHH
Confidence            33444455555555555555433 21 1133344445555555555543    455555554 1  223 3444555555


Q ss_pred             HHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           97 LLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        97 ~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      .+.+.                .| +...+..+..++.+.|++++|...++.+.+..|+.
T Consensus       293 ~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~  351 (656)
T PRK15174        293 ALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVT  351 (656)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc
Confidence            44443                22 33455555566666666666666666665555544

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.23  E-value=2.6e-05  Score=65.21  Aligned_cols=135  Identities=10%  Similarity=-0.039  Sum_probs=104.3

Q ss_pred             chHHHHhccCCC--CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGIID--KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...|+.+..  |+...+..+..++.+.|++++|...|++... ..  |+ ...+..+.......|++++|...++..
T Consensus       526 eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~-l~--P~~~~l~~~La~~l~~~Gr~~eAl~~~~~A  602 (987)
T PRK09782        526 ATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQ-RG--LGDNALYWWLHAQRYIPGQPELALNDLTRS  602 (987)
T ss_pred             HHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHh-cC--CccHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            578888886543  4455677778889999999999999999876 43  43 333334444455669999999999999


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      .   ...|+...|..+..++.+.                .| +...++.+-.++...|++++|...+++..+..|+++..
T Consensus       603 L---~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a  679 (987)
T PRK09782        603 L---NIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDPAL  679 (987)
T ss_pred             H---HhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHH
Confidence            8   3567788888888877776                44 55678888889999999999999999999999987654


Q ss_pred             c
Q 047113          142 Y  142 (145)
Q Consensus       142 ~  142 (145)
                      +
T Consensus       680 ~  680 (987)
T PRK09782        680 I  680 (987)
T ss_pred             H
Confidence            4

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.21  E-value=5.5e-05  Score=52.15  Aligned_cols=104  Identities=13%  Similarity=0.095  Sum_probs=82.2

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHH-hhccch--HHHHHHHHHHhhhhcCcCccHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFA-CSYSGL--IEEGIKVFDIMVHDFQLDLNLE   89 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~-~~~~~~--~~~a~~~~~~m~~~~~~~~~~~   89 (145)
                      .|...|..|-..|...|++++|...|+....   +.| |...+..+-.+ +.+.|+  .++|.+++++.. +  ..|+  
T Consensus        71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~---l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al-~--~dP~--  142 (198)
T PRK10370         71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQ---LRGENAELYAALATVLYYQAGQHMTPQTREMIDKAL-A--LDAN--  142 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHH-H--hCCC--
Confidence            4778899999999999999999999998765   445 56677776665 356666  489999999888 3  3332  


Q ss_pred             HHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           90 HYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        90 ~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                                    +..++..+-..+...|++++|...|+++.+..|.+.
T Consensus       143 --------------~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~~~  178 (198)
T PRK10370        143 --------------EVTALMLLASDAFMQADYAQAIELWQKVLDLNSPRV  178 (198)
T ss_pred             --------------ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCc
Confidence                          666777788889999999999999999998766544

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.19  E-value=5.7e-05  Score=55.13  Aligned_cols=117  Identities=15%  Similarity=-0.002  Sum_probs=68.6

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccH---HH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNL---EH   90 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~---~~   90 (145)
                      +...|+.+-..+.+.|++++|...|+...+   +.| +..+|..+-.++...|++++|.+.|+... +  ..|+-   ..
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~---l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al-~--~~P~~~~~~~  170 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLE---LDPTYNYAYLNRGIALYYGGRYELAQDDLLAFY-Q--DDPNDPYRAL  170 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H--hCCCCHHHHH
Confidence            456677777777777777777777776644   344 34455556666666666666666665554 1  11211   11


Q ss_pred             HHHHHH------------------------------HHhcC---------------------CCchhhHHHHHHHHHhcc
Q 047113           91 YGITVD------------------------------LLATG---------------------ETEPYVWGALLGACRIHH  119 (145)
Q Consensus        91 ~~~li~------------------------------~~~~~---------------------~p~~~~~~~li~~~~~~g  119 (145)
                      |..+..                              .+...                     +.....|..+-..+...|
T Consensus       171 ~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~~~~~~~~lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g  250 (296)
T PRK11189        171 WLYLAESKLDPKQAKENLKQRYEKLDKEQWGWNIVEFYLGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLG  250 (296)
T ss_pred             HHHHHHccCCHHHHHHHHHHHHhhCCccccHHHHHHHHccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCC
Confidence            111110                              00000                     112346777888888899


Q ss_pred             ChhHHHHHHccCCCCCCC
Q 047113          120 NVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       120 ~~~~a~~~~~~~~~~~~~  137 (145)
                      ++++|...|++..+.+|+
T Consensus       251 ~~~~A~~~~~~Al~~~~~  268 (296)
T PRK11189        251 DLDEAAALFKLALANNVY  268 (296)
T ss_pred             CHHHHHHHHHHHHHhCCc
Confidence            999999999988887763

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

Probab=98.18  E-value=6e-05  Score=48.20  Aligned_cols=105  Identities=15%  Similarity=0.128  Sum_probs=84.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +......+...+.+.|++++|.+.|..... .+ +.+...+..+-..+...|+++.|...++... ..  .|        
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~-~~--~p--------   82 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAA-YD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAA-AL--DP--------   82 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHH-hC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hc--CC--------
Confidence            455667778888999999999999999866 43 3367788889999999999999999999887 32  23        


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                              .+...+..+-..|...|++++|...+++..+..|+++.
T Consensus        83 --------~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~  120 (135)
T TIGR02552        83 --------DDPRPYFHAAECLLALGEPESALKALDLAIEICGENPE  120 (135)
T ss_pred             --------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccch
Confidence                    24555666677888899999999999999998887654

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

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

Probab=98.18  E-value=1e-05  Score=58.36  Aligned_cols=126  Identities=10%  Similarity=0.090  Sum_probs=82.5

Q ss_pred             hHHHHhccCC-----CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            3 DAERIFGGII-----DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m~-----~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++.++++...     +++...|..+...+.+.|++++|.++|++..+   ..| |....+.++..+...|+.+++.++++
T Consensus       128 ~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~---~~P~~~~~~~~l~~~li~~~~~~~~~~~l~  204 (280)
T PF13429_consen  128 EAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALE---LDPDDPDARNALAWLLIDMGDYDEAREALK  204 (280)
T ss_dssp             HHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHH---H-TT-HHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHCCChHHHHHHHH
Confidence            4555665532     24677899999999999999999999999865   457 47788999999999999999999999


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ... +.. +.|...|..+..+|...                 +.|......+..++...|+.++|..+.+++.+
T Consensus       205 ~~~-~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  205 RLL-KAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHH-HH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT-----------------
T ss_pred             HHH-HHC-cCHHHHHHHHHHHhcccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            988 332 44566677777777655                 44777888888999999999999999887654

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

Probab=98.17  E-value=5.2e-06  Score=65.22  Aligned_cols=116  Identities=13%  Similarity=0.144  Sum_probs=54.6

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGIT   94 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l   94 (145)
                      +.|..|-..|...|+.|.|+..|++..+   ++|+ ...||.|-.+....|.+.+|.+.+....   .+.|+ ...-+.|
T Consensus       287 ~a~gNla~iYyeqG~ldlAI~~Ykral~---~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL---~l~p~hadam~NL  360 (966)
T KOG4626|consen  287 VAHGNLACIYYEQGLLDLAIDTYKRALE---LQPNFPDAYNNLANALKDKGSVTEAVDCYNKAL---RLCPNHADAMNNL  360 (966)
T ss_pred             hhccceEEEEeccccHHHHHHHHHHHHh---cCCCchHHHhHHHHHHHhccchHHHHHHHHHHH---HhCCccHHHHHHH
Confidence            3444444444444555555555554432   3343 3355555555555555555555555444   22332 3334444


Q ss_pred             HHHHhcC----------------CCch-hhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           95 VDLLATG----------------ETEP-YVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        95 i~~~~~~----------------~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      ..+|...                -|+. ...|.|-..|..+|++++|...+++..++.|..
T Consensus       361 gni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~f  421 (966)
T KOG4626|consen  361 GNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTF  421 (966)
T ss_pred             HHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchH
Confidence            4444433                2322 244555555555555555555555555555543

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

Probab=98.15  E-value=2.5e-05  Score=61.52  Aligned_cols=138  Identities=11%  Similarity=0.075  Sum_probs=79.3

Q ss_pred             hHHHHhccCC--CC-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            3 DAERIFGGII--DK-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         3 ~A~~~f~~m~--~~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      -|...+++.-  .| -...||.|-.|+-..|++.+|.++|.....   +.|+ ..+.+.+-..+.+.|.++.|..+|...
T Consensus       304 lAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~---l~p~hadam~NLgni~~E~~~~e~A~~ly~~a  380 (966)
T KOG4626|consen  304 LAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALR---LCPNHADAMNNLGNIYREQGKIEEATRLYLKA  380 (966)
T ss_pred             HHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHH---hCCccHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            3455555332  12 244566666666666666666666665533   3332 334555555555555555555554443


Q ss_pred             hhh-------------------------------cCcCcc-HHHHHHHHHHHhcC----------------CCch-hhHH
Q 047113           79 VHD-------------------------------FQLDLN-LEHYGITVDLLATG----------------ETEP-YVWG  109 (145)
Q Consensus        79 ~~~-------------------------------~~~~~~-~~~~~~li~~~~~~----------------~p~~-~~~~  109 (145)
                      ..-                               -.+.|+ ...|+.+...|-..                .|.. ...+
T Consensus       381 l~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhs  460 (966)
T KOG4626|consen  381 LEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHS  460 (966)
T ss_pred             HhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHh
Confidence            300                               034443 23333333222222                4443 5788


Q ss_pred             HHHHHHHhccChhHHHHHHccCCCCCCCCCCCcc
Q 047113          110 ALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYT  143 (145)
Q Consensus       110 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  143 (145)
                      .|-..|...|++.+|..-++...+++||.|..|.
T Consensus       461 NLasi~kDsGni~~AI~sY~~aLklkPDfpdA~c  494 (966)
T KOG4626|consen  461 NLASIYKDSGNIPEAIQSYRTALKLKPDFPDAYC  494 (966)
T ss_pred             hHHHHhhccCCcHHHHHHHHHHHccCCCCchhhh
Confidence            8889999999999999999999999998887664

>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=98.15  E-value=5.6e-05  Score=48.40  Aligned_cols=83  Identities=16%  Similarity=0.219  Sum_probs=72.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHh---------------HhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLV---------------IHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m---------------~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      |..++.++|.++++.|+.+....+.+..               +. +.+.|+..+..+++.+++..|++..|..+.+.+.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~-spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs   79 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPS-SPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFS   79 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCC-CCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            5678999999999999999999988764               12 4467899999999999999999999999999999


Q ss_pred             hhcCcCccHHHHHHHHHHH
Q 047113           80 HDFQLDLNLEHYGITVDLL   98 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~   98 (145)
                      ..++++.+..+|..|++=.
T Consensus        80 ~~Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   80 RKYPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             HHcCCCCCHHHHHHHHHHH
Confidence            8899888888898888633

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

>PRK12370 invasion protein regulator; Provisional

Probab=98.14  E-value=7.1e-05  Score=59.17  Aligned_cols=130  Identities=9%  Similarity=-0.060  Sum_probs=92.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|...+++..   +.+...|..+-..+...|++++|...|++..+   +.| +...+..+-..+...|++++|...+++
T Consensus       321 ~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~---l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~  397 (553)
T PRK12370        321 IKAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANL---LSPISADIKYYYGWNLFMAGQLEEALQTINE  397 (553)
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            35666666442   34677898998899999999999999999866   346 466788888889999999999999999


Q ss_pred             hhhhcCcCccH-HHHHHHHH-HHhcC----------------CCch-hhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           78 MVHDFQLDLNL-EHYGITVD-LLATG----------------ETEP-YVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        78 m~~~~~~~~~~-~~~~~li~-~~~~~----------------~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      .. +  +.|+. ..+..+.. .|...                .|+. ..+..+-..+...|++++|...++++....|.
T Consensus       398 Al-~--l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~  473 (553)
T PRK12370        398 CL-K--LDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEIT  473 (553)
T ss_pred             HH-h--cCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccch
Confidence            88 3  34432 22222221 22211                3443 45666777888999999999999887666554

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

Probab=98.08  E-value=7.3e-06  Score=66.36  Aligned_cols=84  Identities=25%  Similarity=0.224  Sum_probs=74.4

Q ss_pred             HHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-------CCchhhHH
Q 047113           37 EAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------ETEPYVWG  109 (145)
Q Consensus        37 ~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-------~p~~~~~~  109 (145)
                      .++..|+. .|+.||-+||..+|.-||..|+++.|- +|..|. -....-+...++.++.+-.+.       .|...+|+
T Consensus        11 nfla~~e~-~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~-~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt   87 (1088)
T KOG4318|consen   11 NFLALHEI-SGILPNRVTYQSLIARYCTKGDIEAAT-IFPFME-IKSLPVREGVFRGLVASHKEANDAENPKEPLADTYT   87 (1088)
T ss_pred             hHHHHHHH-hcCCCchhhHHHHHHHHcccCCCcccc-chhhhh-cccccccchhHHHHHhcccccccccCCCCCchhHHH
Confidence            35667778 999999999999999999999999999 999998 677777899999999876655       77888999


Q ss_pred             HHHHHHHhccChhH
Q 047113          110 ALLGACRIHHNVKI  123 (145)
Q Consensus       110 ~li~~~~~~g~~~~  123 (145)
                      +|+.+|..+|++..
T Consensus        88 ~Ll~ayr~hGDli~  101 (1088)
T KOG4318|consen   88 NLLKAYRIHGDLIL  101 (1088)
T ss_pred             HHHHHHHhccchHH
Confidence            99999999999855

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

Probab=98.06  E-value=3e-05  Score=59.09  Aligned_cols=98  Identities=15%  Similarity=0.034  Sum_probs=78.8

Q ss_pred             chHHHHhccCCC-C-----chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHH
Q 047113            2 DDAERIFGGIID-K-----NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVF   75 (145)
Q Consensus         2 ~~A~~~f~~m~~-~-----~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~   75 (145)
                      |+++.++...+. |     -..|..++|..|.+.|..++++.+++.=.. .|+=||..|||.+|+.+.+.|++..|.++.
T Consensus        83 d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~-yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~  161 (429)
T PF10037_consen   83 DEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQ-YGIFPDNFSFNLLMDHFLKKGNYKSAAKVA  161 (429)
T ss_pred             HHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhh-cccCCChhhHHHHHHHHhhcccHHHHHHHH
Confidence            456666665553 2     124567999999999999999999999888 999999999999999999999999999999


Q ss_pred             HHhhhhcCcCccHHHHHHHHHHHhcC
Q 047113           76 DIMVHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        76 ~~m~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                      ..|. ..+.-.+..|+..-+.+|.+.
T Consensus       162 ~~~~-lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  162 TEMM-LQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHH-HhhccCCchHHHHHHHHHHHh
Confidence            9998 555556666766555555444

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 [].

>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=98.05  E-value=0.00014  Score=42.06  Aligned_cols=98  Identities=16%  Similarity=0.107  Sum_probs=75.9

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      +|..+...+.+.|++++|...|++..+ .. +.+...+..+...+...++++.|...++... +..  |           
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~-~~~--~-----------   65 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALE-LD-PDNADAYYNLAAAYYKLGKYEEALEDYEKAL-ELD--P-----------   65 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHh-cC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCC--C-----------
Confidence            466778888999999999999999865 32 2344677888888899999999999999887 322  2           


Q ss_pred             HhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           98 LATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        98 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                           .+..++..+...+...|++++|...+.+..+..|
T Consensus        66 -----~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~   99 (100)
T cd00189          66 -----DNAKAYYNLGLAYYKLGKYEEALEAYEKALELDP   99 (100)
T ss_pred             -----cchhHHHHHHHHHHHHHhHHHHHHHHHHHHccCC
Confidence                 1335666777888889999999999988766555

>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=98.04  E-value=0.00012  Score=55.45  Aligned_cols=106  Identities=12%  Similarity=0.097  Sum_probs=65.2

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhc
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  100 (145)
                      +|+..+...++++.|..+|+++.+ ..  |+..  ..+...+...++-.+|.+++++....  .+.+......-.+-|.+
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~-~~--pev~--~~LA~v~l~~~~E~~AI~ll~~aL~~--~p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRE-RD--PEVA--VLLARVYLLMNEEVEAIRLLNEALKE--NPQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHh-cC--CcHH--HHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHh
Confidence            444555556677777777777765 33  4433  34555555566666666666666521  12233333322222322


Q ss_pred             C----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113          101 G----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus       101 ~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .                .| +..+|..|..+|...|+++.|+...+-+.-
T Consensus       247 k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  247 KKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             cCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            2                44 556999999999999999999999887654

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

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.95  E-value=0.00017  Score=52.72  Aligned_cols=111  Identities=14%  Similarity=0.033  Sum_probs=79.9

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGI   93 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~   93 (145)
                      ...|..+-..+.+.|++++|...|++..+   +.| +...|+.+-..+...|+++.|...|+...   .+.|+ ...|..
T Consensus        64 a~~~~~~g~~~~~~g~~~~A~~~~~~Al~---l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al---~l~P~~~~a~~~  137 (296)
T PRK11189         64 AQLHYERGVLYDSLGLRALARNDFSQALA---LRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVL---ELDPTYNYAYLN  137 (296)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH---HhCCCCHHHHHH
Confidence            34688888899999999999999999865   345 57899999999999999999999999998   34564 556666


Q ss_pred             HHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           94 TVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        94 li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      +..++...                .|+..........+...++.++|...+++..
T Consensus       138 lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        138 RGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            66655443                4433211111122345677888888886533

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

Probab=97.91  E-value=2.8e-05  Score=61.03  Aligned_cols=56  Identities=13%  Similarity=0.064  Sum_probs=27.1

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      -|...|.+.++++.|+-.|+...+   +-| +.+....+...+-+.|..|+|.+++++..
T Consensus       494 GlG~vy~Kqek~e~Ae~~fqkA~~---INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~  550 (638)
T KOG1126|consen  494 GLGTVYLKQEKLEFAEFHFQKAVE---INPSNSVILCHIGRIQHQLKRKDKALQLYEKAI  550 (638)
T ss_pred             hhhhheeccchhhHHHHHHHhhhc---CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHH
Confidence            344445555555555555544422   333 33344444444455555555555555544

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.89  E-value=5.3e-05  Score=54.62  Aligned_cols=96  Identities=22%  Similarity=0.226  Sum_probs=78.1

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCC
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGE  102 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~  102 (145)
                      +-..+++++++|+..|.+..+   +.| |.+-|..--.+|++.|+++.|.+-.+...   .+.|.               
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~---l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al---~iDp~---------------  147 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIE---LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESAL---SIDPH---------------  147 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHh---cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHH---hcChH---------------
Confidence            445678899999999999876   455 78888999999999999988887666665   23332               


Q ss_pred             CchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          103 TEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       103 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                       -..+|..|-.+|...|++++|.+.|++..+++|++.++
T Consensus       148 -yskay~RLG~A~~~~gk~~~A~~aykKaLeldP~Ne~~  185 (304)
T KOG0553|consen  148 -YSKAYGRLGLAYLALGKYEEAIEAYKKALELDPDNESY  185 (304)
T ss_pred             -HHHHHHHHHHHHHccCcHHHHHHHHHhhhccCCCcHHH
Confidence             45678889999999999999999999999999988754

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.88  E-value=0.00035  Score=57.34  Aligned_cols=138  Identities=9%  Similarity=-0.016  Sum_probs=72.2

Q ss_pred             chHHHHhccCCCC--chh--hHHHHHHHHHHcCChHHHHHHHHHhHhhcC-CCC--cHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIIDK--NVV--IWSGMIASHAIHGQEREALEAFYLVIHCSD-GKP--NNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~~--~~~--~~~~li~a~~~~g~~~~A~~~~~~m~~~~~-~~p--~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.+.|+.+...  +..  .--.+..+|...|++++|+.+|++... .. ..+  .......+..++.+.|++++|.++
T Consensus       254 ~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~-~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~  332 (765)
T PRK10049        254 KDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFY-HPETIADLSDEELADLFYSLLESENYPGALTV  332 (765)
T ss_pred             HHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhh-cCCCCCCCChHHHHHHHHHHHhcccHHHHHHH
Confidence            4566666666431  111  111135567777777777777776544 22 110  123445555566777777777777


Q ss_pred             HHHhhhhcC----------cCcc---HHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHH
Q 047113           75 FDIMVHDFQ----------LDLN---LEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIG  124 (145)
Q Consensus        75 ~~~m~~~~~----------~~~~---~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a  124 (145)
                      ++.+.....          -.|+   ...+..+...+...                 +.+...+..+...+...|++++|
T Consensus       333 l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A  412 (765)
T PRK10049        333 TAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAA  412 (765)
T ss_pred             HHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHH
Confidence            776662210          1123   12222333333322                 33445666666666666666666


Q ss_pred             HHHHccCCCCCCCCCC
Q 047113          125 ELVAKDPFHLDPKNDA  140 (145)
Q Consensus       125 ~~~~~~~~~~~~~~~~  140 (145)
                      +..+++..+..|+++.
T Consensus       413 ~~~l~~al~l~Pd~~~  428 (765)
T PRK10049        413 ENELKKAEVLEPRNIN  428 (765)
T ss_pred             HHHHHHHHhhCCCChH
Confidence            6666666666665543

>PRK12370 invasion protein regulator; Provisional

Probab=97.87  E-value=0.00022  Score=56.40  Aligned_cols=134  Identities=8%  Similarity=-0.087  Sum_probs=93.6

Q ss_pred             chHHHHhccCCC--C-chhhHHHHHHHHH---------HcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchH
Q 047113            2 DDAERIFGGIID--K-NVVIWSGMIASHA---------IHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLI   68 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~~~~~li~a~~---------~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~   68 (145)
                      ++|.+.|++.-+  | +...|..+-.++.         ..+++++|...+++..+   +.| +...+..+-..+...|++
T Consensus       278 ~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~---ldP~~~~a~~~lg~~~~~~g~~  354 (553)
T PRK12370        278 QQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE---LDHNNPQALGLLGLINTIHSEY  354 (553)
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHccCH
Confidence            467777876543  3 4556766655444         23458999999999866   446 577888888888999999


Q ss_pred             HHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC----------------CCch-hhHHHHHHHHHhccChhHHHHHHcc
Q 047113           69 EEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG----------------ETEP-YVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        69 ~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~~-~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      ++|...+++.. +  ..| +...|..+..+|...                .|+. ..+..++..+...|++++|...+++
T Consensus       355 ~~A~~~~~~Al-~--l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~  431 (553)
T PRK12370        355 IVGSLLFKQAN-L--LSPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDE  431 (553)
T ss_pred             HHHHHHHHHHH-H--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHH
Confidence            99999999998 3  345 466677776666655                4543 3344455567778999999999998


Q ss_pred             CCCC-CCCCCCC
Q 047113          131 PFHL-DPKNDAY  141 (145)
Q Consensus       131 ~~~~-~~~~~~~  141 (145)
                      +.+. .|+++..
T Consensus       432 ~l~~~~p~~~~~  443 (553)
T PRK12370        432 LRSQHLQDNPIL  443 (553)
T ss_pred             HHHhccccCHHH
Confidence            7664 3555543

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.81  E-value=0.00038  Score=52.93  Aligned_cols=34  Identities=18%  Similarity=0.316  Sum_probs=21.6

Q ss_pred             hhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113          105 PYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus       105 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      .....++-..|.+.|++++|.+.|+...+..|++
T Consensus       328 ~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~  361 (398)
T PRK10747        328 PLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDA  361 (398)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCH
Confidence            3445566666666677777777776666666644

>TIGR00540 hemY_coli hemY protein

Probab=97.77  E-value=0.0016  Score=49.68  Aligned_cols=134  Identities=11%  Similarity=-0.079  Sum_probs=95.8

Q ss_pred             chHHHHhccCCC--Cch--hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIID--KNV--VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~--~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|....+  |+.  ..--.....+.+.|++++|...++.+.+ .  .| +....-.+...+.+.|+++.+.+++.
T Consensus       135 ~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~-~--~P~~~~~l~ll~~~~~~~~d~~~a~~~l~  211 (409)
T TIGR00540       135 ARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHGVDKLLE-M--APRHKEVLKLAEEAYIRSGAWQALDDIID  211 (409)
T ss_pred             HHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHH-h--CCCCHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            345566655421  332  2333346777789999999999999977 3  35 66688899999999999999999999


Q ss_pred             HhhhhcCcCccHH-------HHHHHHHH------------HhcCC-----CchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           77 IMVHDFQLDLNLE-------HYGITVDL------------LATGE-----TEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        77 ~m~~~~~~~~~~~-------~~~~li~~------------~~~~~-----p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      .+. +.+..+...       .+..++..            +.+..     .+...+-.+...+...|+.++|..+.++..
T Consensus       212 ~l~-k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l  290 (409)
T TIGR00540       212 NMA-KAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGL  290 (409)
T ss_pred             HHH-HcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            999 665433221       12222211            11113     377889999999999999999999999999


Q ss_pred             CCCCCCC
Q 047113          133 HLDPKND  139 (145)
Q Consensus       133 ~~~~~~~  139 (145)
                      +..|++.
T Consensus       291 ~~~pd~~  297 (409)
T TIGR00540       291 KKLGDDR  297 (409)
T ss_pred             hhCCCcc
Confidence            8888665

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.77  E-value=0.00065  Score=58.16  Aligned_cols=74  Identities=15%  Similarity=0.092  Sum_probs=53.4

Q ss_pred             chHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            2 DDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         2 ~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ++|.++++. .+.+...+..+-..+.+.|++++|...|+...+ .  .| +...+..+...+...|++++|...++...
T Consensus       590 ~eA~~~l~~-~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~-~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll  664 (1157)
T PRK11447        590 AEAEALLRQ-QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLT-R--EPGNADARLGLIEVDIAQGDLAAARAQLAKLP  664 (1157)
T ss_pred             HHHHHHHHh-CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            355666662 223555667777888888888888888888765 2  34 56677888888888888888888888766

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.74  E-value=0.0011  Score=41.00  Aligned_cols=107  Identities=12%  Similarity=0.037  Sum_probs=79.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcC-CCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSD-GKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      .++-.+...+.+.|++++|...|..+.. .. -.| ....+..+..++.+.|+++.|...++.+....   |+.      
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~---p~~------   72 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLK-KYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKY---PKS------   72 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH-HCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHC---CCC------
Confidence            3566778888999999999999999876 32 111 13466678888999999999999999988322   220      


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                             +....++..+...+...|+.++|...++++.+..|+++.
T Consensus        73 -------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~  111 (119)
T TIGR02795        73 -------PKAPDALLKLGMSLQELGDKEKAKATLQQVIKRYPGSSA  111 (119)
T ss_pred             -------CcccHHHHHHHHHHHHhCChHHHHHHHHHHHHHCcCChh
Confidence                   011334555667788899999999999999888886653

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.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.73  E-value=0.00017  Score=54.04  Aligned_cols=95  Identities=14%  Similarity=0.096  Sum_probs=64.1

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCC
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGE  102 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~  102 (145)
                      ....+.|++++|+.+|++..+   ..| +...|..+-.++.+.|+++.|...+++.. .  +.|+               
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~---~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al-~--l~P~---------------   68 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAID---LDPNNAELYADRAQANIKLGNFTEAVADANKAI-E--LDPS---------------   68 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCcC---------------
Confidence            445667788888888887755   234 45667777777777888888888777777 2  2332               


Q ss_pred             CchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113          103 TEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus       103 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                       +...|..+-.+|...|++++|...+++..++.|+++.
T Consensus        69 -~~~a~~~lg~~~~~lg~~~eA~~~~~~al~l~P~~~~  105 (356)
T PLN03088         69 -LAKAYLRKGTACMKLEEYQTAKAALEKGASLAPGDSR  105 (356)
T ss_pred             -CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCHH
Confidence             3445555666777777777777777777777766554

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.68  E-value=0.00028  Score=57.93  Aligned_cols=125  Identities=8%  Similarity=-0.034  Sum_probs=88.0

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.++|....+   .+...+..+..++.+.|++++|..+|++...   ..| +...+..+...+...|++++|...++.
T Consensus        32 ~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~la~~l~~~g~~~eA~~~l~~  108 (765)
T PRK10049         32 AEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALS---LEPQNDDYQRGLILTLADAGQYDEALVKAKQ  108 (765)
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            467777776643   2444688888899999999999999988755   234 455667777788889999999999998


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .. ..  .| +.. +..+..++...                .| +...+..+...+...|..++|+..++....
T Consensus       109 ~l-~~--~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~  178 (765)
T PRK10049        109 LV-SG--APDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDANL  178 (765)
T ss_pred             HH-Hh--CCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCC
Confidence            87 22  33 344 66666555554                33 444556666777777787888877776654

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.67  E-value=0.00068  Score=58.05  Aligned_cols=117  Identities=14%  Similarity=0.129  Sum_probs=76.8

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH---
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD---   96 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~---   96 (145)
                      .+-.++.+.|++++|+..|++..+   ..| |...+..+-.++.+.|++++|...|++......-.+....|..++.   
T Consensus       274 ~~G~~~~~~g~~~~A~~~l~~aL~---~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~  350 (1157)
T PRK11447        274 AQGLAAVDSGQGGKAIPELQQAVR---ANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNR  350 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhh
Confidence            334566778888888888888755   235 5677777778888888888888888887722211112222222221   


Q ss_pred             ---------HHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           97 ---------LLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        97 ---------~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                               .+.+.                 +.+...+..+-..+...|++++|++.|++..+..|+++.
T Consensus       351 ~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~  420 (1157)
T PRK11447        351 YWLLIQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTN  420 (1157)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH
Confidence                     11111                 335567777888888889999999999888888776543

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=97.65  E-value=0.0024  Score=49.00  Aligned_cols=127  Identities=13%  Similarity=0.091  Sum_probs=100.6

Q ss_pred             chHHHHhccCCC--C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|+..++.+..  | |..-+......+.+.|+.++|.+.++.+..   ..|+ ..-.-.+-.++.+.|+..+|..++..
T Consensus       323 d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~---l~P~~~~l~~~~a~all~~g~~~eai~~L~~  399 (484)
T COG4783         323 DEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALA---LDPNSPLLQLNLAQALLKGGKPQEAIRILNR  399 (484)
T ss_pred             chHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHh---cCCCccHHHHHHHHHHHhcCChHHHHHHHHH
Confidence            567777776632  4 566677788899999999999999999854   5676 44556677788899999999999988


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      -.  .....|...|..|-.+|.+.......--+.-.+|...|+++.|........+
T Consensus       400 ~~--~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~~~~G~~~~A~~~l~~A~~  453 (484)
T COG4783         400 YL--FNDPEDPNGWDLLAQAYAELGNRAEALLARAEGYALAGRLEQAIIFLMRASQ  453 (484)
T ss_pred             Hh--hcCCCCchHHHHHHHHHHHhCchHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            87  3446678899999999999865666666777888999999999888887665

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

Probab=97.61  E-value=0.0011  Score=56.60  Aligned_cols=126  Identities=14%  Similarity=0.202  Sum_probs=94.0

Q ss_pred             chHHHHhccCCC--------CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH-HHHHHHHHHhhccchHHHHH
Q 047113            2 DDAERIFGGIID--------KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN-VTFLSILFACSYSGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m~~--------~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~-~~~~~ll~~~~~~~~~~~a~   72 (145)
                      ++|++++++..+        --...|-++++.-...|.-+...++|++..+    -.|+ ..|..|...|.+.+.++.|.
T Consensus      1475 ekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcq----ycd~~~V~~~L~~iy~k~ek~~~A~ 1550 (1710)
T KOG1070|consen 1475 EKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQ----YCDAYTVHLKLLGIYEKSEKNDEAD 1550 (1710)
T ss_pred             HHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHH----hcchHHHHHHHHHHHHHhhcchhHH
Confidence            567777775432        1345788888877777888888888888765    3343 36788888888888888888


Q ss_pred             HHHHHhhhhcCcCccHHHHHHHHHHHhcC---------------------------------------------------
Q 047113           73 KVFDIMVHDFQLDLNLEHYGITVDLLATG---------------------------------------------------  101 (145)
Q Consensus        73 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~---------------------------------------------------  101 (145)
                      ++++.|.++.|  ....+|..+++.+.+.                                                   
T Consensus      1551 ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ 1628 (1710)
T KOG1070|consen 1551 ELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLS 1628 (1710)
T ss_pred             HHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHh
Confidence            88888886666  6677777777777665                                                   


Q ss_pred             --CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113          102 --ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus       102 --~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                        +.-...|+..|+.=.++|+.+.++.+|++...
T Consensus      1629 ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~ 1662 (1710)
T KOG1070|consen 1629 AYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIE 1662 (1710)
T ss_pred             hCccchhHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence              22445788889988999999999999988765

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.61  E-value=0.00058  Score=56.36  Aligned_cols=131  Identities=9%  Similarity=0.028  Sum_probs=86.2

Q ss_pred             chHHHHhccCCC--Cch--hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH---HHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID--KNV--VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV---TFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~--~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~---~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|...|++..+  |+.  ..+ .++..+...|+.++|...+++..     .|+..   ....+...+...|++++|.++
T Consensus        51 ~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~-----~p~n~~~~~llalA~ly~~~gdyd~Aiel  124 (822)
T PRK14574         51 APVLDYLQEESKAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQ-----SSMNISSRGLASAARAYRNEKRWDQALAL  124 (822)
T ss_pred             HHHHHHHHHHHhhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhc-----cCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            456777776643  332  233 88888888899999988888764     24322   223334567788999999999


Q ss_pred             HHHhhhhcCcCc-cHHHHHHHHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           75 FDIMVHDFQLDL-NLEHYGITVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        75 ~~~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ++.+. +  ..| +...+..++..|.+.                .|+...+-.++..+...++..+|++.++++.+..|+
T Consensus       125 y~kaL-~--~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~P~  201 (822)
T PRK14574        125 WQSSL-K--KDPTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAVRLAPT  201 (822)
T ss_pred             HHHHH-h--hCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhCCC
Confidence            99888 2  233 355556666666655                556555544444444466666688999988888887


Q ss_pred             CCCC
Q 047113          138 NDAY  141 (145)
Q Consensus       138 ~~~~  141 (145)
                      ++..
T Consensus       202 n~e~  205 (822)
T PRK14574        202 SEEV  205 (822)
T ss_pred             CHHH
Confidence            7654

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.58  E-value=0.001  Score=43.46  Aligned_cols=76  Identities=8%  Similarity=-0.002  Sum_probs=65.0

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+-.++.+.|++++|...|+.... .+ +.+...+..+-.++.+.|+.++|...|+..
T Consensus        41 ~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~-l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~~A  118 (144)
T PRK15359         41 SRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALM-LD-ASHPEPVYQTGVCLKMMGEPGLAREAFQTA  118 (144)
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-cC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            56788888553   34778999999999999999999999999876 33 237788999999999999999999999998


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       119 l  119 (144)
T PRK15359        119 I  119 (144)
T ss_pred             H
Confidence            8

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.56  E-value=0.0017  Score=43.51  Aligned_cols=64  Identities=14%  Similarity=0.235  Sum_probs=53.1

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc--HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN--NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ....|..+...+.+.|++++|...|++... ..-.+.  ...+..+-..+.+.|+++.|...+.+..
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al   99 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALK-LEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQAL   99 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            445788888999999999999999999865 332332  4578888899999999999999999888

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=97.52  E-value=0.0027  Score=46.12  Aligned_cols=95  Identities=14%  Similarity=0.067  Sum_probs=80.2

Q ss_pred             HHHhccCC--CCchhhHHHHHHHHHHc-----CChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchH---------
Q 047113            5 ERIFGGII--DKNVVIWSGMIASHAIH-----GQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLI---------   68 (145)
Q Consensus         5 ~~~f~~m~--~~~~~~~~~li~a~~~~-----g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~---------   68 (145)
                      ++.|...+  ++|-.+|=+++..+..+     +.++=....++.|++ .|+..|..+|+.||..+-+..-+         
T Consensus        54 e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~e-yGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F  132 (406)
T KOG3941|consen   54 EKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKE-YGVERDLDVYKGLLNVFPKGKFIPQNVFQKVF  132 (406)
T ss_pred             hhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHH-hcchhhHHHHHHHHHhCcccccccHHHHHHHH
Confidence            45677666  57888899999888754     567778888999999 99999999999999998775432         


Q ss_pred             -------HHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC
Q 047113           69 -------EEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        69 -------~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                             +=+..++++|. ..|+.||-.+-..|++++++.
T Consensus       133 ~HYP~QQ~C~I~vLeqME-~hGVmPdkE~e~~lvn~FGr~  171 (406)
T KOG3941|consen  133 LHYPQQQNCAIKVLEQME-WHGVMPDKEIEDILVNAFGRW  171 (406)
T ss_pred             hhCchhhhHHHHHHHHHH-HcCCCCchHHHHHHHHHhccc
Confidence                   34788999999 999999999999999999988

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.52  E-value=0.0041  Score=47.32  Aligned_cols=131  Identities=8%  Similarity=-0.011  Sum_probs=88.5

Q ss_pred             chHHHHhccCCC--CchhhHH--HHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIID--KNVVIWS--GMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~~~~~--~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      +.|...|.++.+  |+....-  .....+.+.|++++|...+++..+ .  .| +......+...+.+.|+|+++..++.
T Consensus       135 ~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~-~--~P~~~~al~ll~~~~~~~gdw~~a~~~l~  211 (398)
T PRK10747        135 ARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGVDKLLE-V--APRHPEVLRLAEQAYIRTGAWSSLLDILP  211 (398)
T ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-c--CCCCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            456777776644  3332222  235577889999999999999866 3  35 57788899999999999999999999


Q ss_pred             HhhhhcCcC-ccH------HHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           77 IMVHDFQLD-LNL------EHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        77 ~m~~~~~~~-~~~------~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      .+. +.+.. |..      ..|..++....+.                 +.+......+..++...|+.++|..+.++..
T Consensus       212 ~l~-k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l  290 (398)
T PRK10747        212 SMA-KAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGL  290 (398)
T ss_pred             HHH-HcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999 44433 221      1222222211111                 4466677778888888888888888888766


Q ss_pred             CCCC
Q 047113          133 HLDP  136 (145)
Q Consensus       133 ~~~~  136 (145)
                      +..+
T Consensus       291 ~~~~  294 (398)
T PRK10747        291 KRQY  294 (398)
T ss_pred             hcCC
Confidence            6333

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

Probab=97.44  E-value=0.0018  Score=40.46  Aligned_cols=63  Identities=11%  Similarity=0.094  Sum_probs=53.5

Q ss_pred             HHHHHHHHhhccchHHHHHHHHHHhhhhcCc-CccHHHHHHHHHHHhcC--------------------------CCchh
Q 047113           54 TFLSILFACSYSGLIEEGIKVFDIMVHDFQL-DLNLEHYGITVDLLATG--------------------------ETEPY  106 (145)
Q Consensus        54 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~~~~~li~~~~~~--------------------------~p~~~  106 (145)
                      |-...|.-|...+++...-.+|+.++ +.|+ .|++.+|+.++++.++.                          +|+..
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslk-RN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~e  105 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLK-RNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDE  105 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHH-hcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHH
Confidence            44567777888899999999999999 9999 99999999999999877                          77778


Q ss_pred             hHHHHHHHHHh
Q 047113          107 VWGALLGACRI  117 (145)
Q Consensus       107 ~~~~li~~~~~  117 (145)
                      +|+.++....+
T Consensus       106 tYnivl~~Llk  116 (120)
T PF08579_consen  106 TYNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHHH
Confidence            88877776644

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 [, , ].

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

Probab=97.44  E-value=0.00055  Score=50.47  Aligned_cols=138  Identities=11%  Similarity=0.058  Sum_probs=101.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.++++..-   +.++..-.++-..|.-.++++-|++.|+++.+ .|+. +..-|+.+--+|.-.+++|.+..-|.+.
T Consensus       307 ~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLq-mG~~-speLf~NigLCC~yaqQ~D~~L~sf~RA  384 (478)
T KOG1129|consen  307 EDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQ-MGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQRA  384 (478)
T ss_pred             HHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHH-hcCC-ChHHHhhHHHHHHhhcchhhhHHHHHHH
Confidence            45666666442   23666777778888889999999999999998 8876 7888888888999999999999888887


Q ss_pred             hhhcCcCcc--HHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           79 VHDFQLDLN--LEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        79 ~~~~~~~~~--~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      .+ .--.|+  ..+|..|-...+..                 .....++|.|----.+.|+++.|+.++.-.+.+.|+..
T Consensus       385 ls-tat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~~P~m~  463 (478)
T KOG1129|consen  385 LS-TATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSVMPDMA  463 (478)
T ss_pred             Hh-hccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhhCcccc
Confidence            73 222232  34444443222211                 44667899988888899999999999999888888755


Q ss_pred             CCc
Q 047113          140 AYY  142 (145)
Q Consensus       140 ~~~  142 (145)
                      ...
T Consensus       464 E~~  466 (478)
T KOG1129|consen  464 EVT  466 (478)
T ss_pred             ccc
Confidence            443

>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=97.42  E-value=0.0017  Score=45.19  Aligned_cols=73  Identities=19%  Similarity=0.217  Sum_probs=65.7

Q ss_pred             CCCcHHHHHHHHHHhhc-----cchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC---------------------
Q 047113           48 GKPNNVTFLSILFACSY-----SGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG---------------------  101 (145)
Q Consensus        48 ~~p~~~~~~~ll~~~~~-----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~---------------------  101 (145)
                      -..|-.+|..+++.+.+     .|.++.....++.|. +.|++-|..+|+.||+.+-+.                     
T Consensus        43 ~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~-efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c  121 (228)
T PF06239_consen   43 QAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMD-EFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQEC  121 (228)
T ss_pred             ccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHH-HcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHH
Confidence            45688899999999865     588999999999999 999999999999999999988                     


Q ss_pred             -------------CCchhhHHHHHHHHHhccCh
Q 047113          102 -------------ETEPYVWGALLGACRIHHNV  121 (145)
Q Consensus       102 -------------~p~~~~~~~li~~~~~~g~~  121 (145)
                                   -||..++..|++.+++.+..
T Consensus       122 ~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  122 AIDLLEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence                         89999999999999987654

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

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=97.40  E-value=0.012  Score=41.96  Aligned_cols=113  Identities=12%  Similarity=0.065  Sum_probs=84.6

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      |...-+.++....++|++.+|...|++...  .-++|...||.+--+|.+.|+++.|..-|.+..+-.+=+|. ..-|.-
T Consensus        99 d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~--l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~-~~nNlg  175 (257)
T COG5010          99 DRELLAAQGKNQIRNGNFGEAVSVLRKAAR--LAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPS-IANNLG  175 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhc--cCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCch-hhhhHH
Confidence            555667788899999999999999999864  34668999999999999999999999999888832222222 222233


Q ss_pred             HHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           95 VDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        95 i~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      +..+.+.                .-|..+-..|..+....|++++|+.+...
T Consensus       176 ms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~  227 (257)
T COG5010         176 MSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQ  227 (257)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhccc
Confidence            3333333                33777888889999999999999988765

>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=97.40  E-value=8.9e-05  Score=41.74  Aligned_cols=61  Identities=16%  Similarity=0.165  Sum_probs=48.8

Q ss_pred             hccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           63 SYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        63 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      .+.|++++|..+|+.+. ..  .|                .+...+-.+..+|.+.|++++|..+++++....|+++.++
T Consensus         2 l~~~~~~~A~~~~~~~l-~~--~p----------------~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~   62 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKAL-QR--NP----------------DNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQ   62 (68)
T ss_dssp             HHTTHHHHHHHHHHHHH-HH--TT----------------TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHH
T ss_pred             hhccCHHHHHHHHHHHH-HH--CC----------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHH
Confidence            35789999999999998 22  33                2666777889999999999999999999999998765443

...

>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=97.39  E-value=0.0014  Score=36.65  Aligned_cols=62  Identities=18%  Similarity=0.226  Sum_probs=47.5

Q ss_pred             HHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           27 AIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        27 ~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      .+.|++++|.++|+.... .  .| |...+..+..++.+.|++++|..+++.+.   ...|+-..|..+
T Consensus         2 l~~~~~~~A~~~~~~~l~-~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~---~~~~~~~~~~~l   64 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQ-R--NPDNPEARLLLAQCYLKQGQYDEAEELLERLL---KQDPDNPEYQQL   64 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHH-H--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCH---GGGTTHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHH-H--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---HHCcCHHHHHHH
Confidence            468999999999999865 3  35 67788889999999999999999999998   234553444433

...

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.37  E-value=0.0039  Score=48.85  Aligned_cols=104  Identities=18%  Similarity=0.170  Sum_probs=83.4

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCC--CC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHC---SDG--KP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEH   90 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~--~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   90 (145)
                      .+++.|-..|-..|++++|.++|+.....   .+.  .+ ....++.+-..|-+.+.++.+.++|.+-. .         
T Consensus       368 ~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~-~---------  437 (508)
T KOG1840|consen  368 KIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAK-D---------  437 (508)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHH-H---------
Confidence            47999999999999999999999986431   222  22 35678999999999999999999998877 1         


Q ss_pred             HHHHHHHHhcCCCch-hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           91 YGITVDLLATGETEP-YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        91 ~~~li~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                        .+ ..++-..|++ .+|..|...|.+.|++++|.++.+.+..
T Consensus       438 --i~-~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  438 --IM-KLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             --HH-HHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence              12 4455556665 6899999999999999999999988764

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

Probab=97.36  E-value=0.002  Score=47.09  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=14.1

Q ss_pred             hhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          105 PYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       105 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ..+.|.+.-+....|++++|.+++.+..+.+|.
T Consensus       201 ~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~  233 (290)
T PF04733_consen  201 PKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN  233 (290)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC
Confidence            334444444444455555555554444444443

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.34  E-value=0.0058  Score=50.65  Aligned_cols=134  Identities=10%  Similarity=-0.006  Sum_probs=86.5

Q ss_pred             chHHHHhccCCC---------CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCC-----------CCcH---HHHHHH
Q 047113            2 DDAERIFGGIID---------KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDG-----------KPNN---VTFLSI   58 (145)
Q Consensus         2 ~~A~~~f~~m~~---------~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~-----------~p~~---~~~~~l   58 (145)
                      ++|..++..+-.         ++......|.-|+...+++++|..+++.+.. ..-           .||.   ..+..+
T Consensus       344 ~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~-~~p~~~~~~~~~~~~pn~d~~~~~~l~  422 (822)
T PRK14574        344 EKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSE-QTPYQVGVYGLPGKEPNDDWIEGQTLL  422 (822)
T ss_pred             HHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHh-cCCcEEeccCCCCCCCCccHHHHHHHH
Confidence            467777776522         1223356778888888888888888888765 211           1221   123445


Q ss_pred             HHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccC
Q 047113           59 LFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHN  120 (145)
Q Consensus        59 l~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~  120 (145)
                      ...+.-.|+.++|++.++.+. .  .-| |......+.+.+...                 +.+..+......++-..|+
T Consensus       423 a~~~~~~gdl~~Ae~~le~l~-~--~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e  499 (822)
T PRK14574        423 VQSLVALNDLPTAQKKLEDLS-S--TAPANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQE  499 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHH-H--hCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhh
Confidence            666777888888888888887 2  233 566666666666655                 3344566677777777788


Q ss_pred             hhHHHHHHccCCCCCCCCC
Q 047113          121 VKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       121 ~~~a~~~~~~~~~~~~~~~  139 (145)
                      +++|..+.+.+.+..|+++
T Consensus       500 ~~~A~~~~~~l~~~~Pe~~  518 (822)
T PRK14574        500 WHQMELLTDDVISRSPEDI  518 (822)
T ss_pred             HHHHHHHHHHHHhhCCCch
Confidence            8888887777777766654

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

Probab=97.34  E-value=0.00084  Score=51.37  Aligned_cols=99  Identities=13%  Similarity=0.123  Sum_probs=58.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC--CCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSD--GKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      ......+++.+....+.+++..++...+. +.  ...-..|..++|..|-+.|..+.+..++..=. .+|+=|       
T Consensus        66 ~~dld~fvn~~~~~~~~d~~~~~L~k~R~-s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~-~yGiF~-------  136 (429)
T PF10037_consen   66 SLDLDIFVNNVESKDDLDEVEDVLYKFRH-SPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRL-QYGIFP-------  136 (429)
T ss_pred             HHHHHHHHhhcCCHhHHHHHHHHHHHHHc-CcccccccCccHHHHHHHHHhcCCHHHHHHHHhChh-hcccCC-------
Confidence            34455556666666666666666666554 31  11122344566666666666666666666665 666655       


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                                |.+|+|.||+.+.+.|++..|.++.-.|..
T Consensus       137 ----------D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~l  166 (429)
T PF10037_consen  137 ----------DNFSFNLLMDHFLKKGNYKSAAKVATEMML  166 (429)
T ss_pred             ----------ChhhHHHHHHHHhhcccHHHHHHHHHHHHH
Confidence                      566666666666777777766666665443

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 [].

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

Probab=97.34  E-value=0.00049  Score=56.52  Aligned_cols=120  Identities=18%  Similarity=0.214  Sum_probs=93.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.++|...-   +.|...=|-+--.++..|++++|..+|.+.++ ... -+..+|-.+-++|...|+|-.|.+.|+..
T Consensus       629 ~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrE-a~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~  706 (1018)
T KOG2002|consen  629 EKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVRE-ATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENC  706 (1018)
T ss_pred             HHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHH-HHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHH
Confidence            57888888553   35777888888889999999999999999987 543 25568888999999999999999999998


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      .++..-.                 .+..+.+.|-+++-+.|++.+|.+.........|.++.
T Consensus       707 lkkf~~~-----------------~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~  751 (1018)
T KOG2002|consen  707 LKKFYKK-----------------NRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTS  751 (1018)
T ss_pred             HHHhccc-----------------CCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccch
Confidence            8554422                 25556666777888888888888887777777776553

>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=97.32  E-value=0.0029  Score=41.10  Aligned_cols=73  Identities=14%  Similarity=0.180  Sum_probs=54.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh----hcCcCccHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH----DFQLDLNLEHYG   92 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~~~~~   92 (145)
                      ....++..+...|++++|..+.+.... .. +.|...|-.+|.++...|+...|.++|+.+..    +.|+.|+..+-.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~-~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALA-LD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH-HS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            456777788889999999999999876 33 33888999999999999999999999998763    468999877644

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

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

Probab=97.31  E-value=0.0017  Score=38.14  Aligned_cols=81  Identities=14%  Similarity=0.167  Sum_probs=46.4

Q ss_pred             cCChHHHHHHHHHhHhhcCC-CCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhh
Q 047113           29 HGQEREALEAFYLVIHCSDG-KPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYV  107 (145)
Q Consensus        29 ~g~~~~A~~~~~~m~~~~~~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~  107 (145)
                      .|++++|+..|+.+.. ..- .|+...+-.+-.++.+.|++++|..+++. . ..+  |+                +...
T Consensus         2 ~~~y~~Ai~~~~k~~~-~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~-~~~--~~----------------~~~~   60 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLE-LDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-L-KLD--PS----------------NPDI   60 (84)
T ss_dssp             TT-HHHHHHHHHHHHH-HHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-H-THH--HC----------------HHHH
T ss_pred             CccHHHHHHHHHHHHH-HCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-h-CCC--CC----------------CHHH
Confidence            5677788888877765 322 22344444467777778888888777777 3 111  11                1111


Q ss_pred             HHHHHHHHHhccChhHHHHHHcc
Q 047113          108 WGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus       108 ~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      .-.+-.+|...|++++|...+++
T Consensus        61 ~~l~a~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   61 HYLLARCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHhc
Confidence            12235666777777777777653

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

Probab=97.30  E-value=0.0042  Score=45.75  Aligned_cols=78  Identities=13%  Similarity=0.164  Sum_probs=51.9

Q ss_pred             chHHHHhccCCCCchhh---HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHH--HHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIIDKNVVI---WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVT--FLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~~~~~~---~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~--~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      |||..+|-+|-.-|..|   .=+|-+.|-+.|..|+|+++-.-+...-++..+...  .--+-.-|...|.+|+|+.+|.
T Consensus        52 dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~  131 (389)
T COG2956          52 DKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFN  131 (389)
T ss_pred             chHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            68888888886544444   446778888888888888888876551222222222  2234455677888888888888


Q ss_pred             Hhh
Q 047113           77 IMV   79 (145)
Q Consensus        77 ~m~   79 (145)
                      .+.
T Consensus       132 ~L~  134 (389)
T COG2956         132 QLV  134 (389)
T ss_pred             HHh
Confidence            887

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.30  E-value=0.0051  Score=50.08  Aligned_cols=110  Identities=10%  Similarity=0.006  Sum_probs=66.7

Q ss_pred             chHHHHhccCCC--C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      |+|.++++...+  | +...+-.+..++.+.+++++|+...++...   ..| +....+.+-.++.+.|.+++|..+|++
T Consensus       103 ~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~---~~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~  179 (694)
T PRK15179        103 DEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFS---GGSSSAREILLEAKSWDEIGQSEQADACFER  179 (694)
T ss_pred             HHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhh---cCCCCHHHHHHHHHHHHHhcchHHHHHHHHH
Confidence            456666664432  3 344566666677777777777777766543   334 344556666666667777777777777


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .. ..  .|+                +...+..+-.++...|+.++|...|+...+
T Consensus       180 ~~-~~--~p~----------------~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        180 LS-RQ--HPE----------------FENGYVGWAQSLTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             HH-hc--CCC----------------cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            66 21  111                234566666667777777777777776554

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.29  E-value=0.00061  Score=37.98  Aligned_cols=61  Identities=20%  Similarity=0.195  Sum_probs=49.1

Q ss_pred             HHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           60 FACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ..+.+.|++++|...|+... +..  |+                +...|..+-..+...|++++|...++++.+..|++|
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l-~~~--P~----------------~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~p   65 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQAL-KQD--PD----------------NPEAWYLLGRILYQQGRYDEALAYYERALELDPDNP   65 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHH-CCS--TT----------------HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHHHcCCHHHHHHHHHHHH-HHC--CC----------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCC
Confidence            45678999999999999999 333  43                556777788899999999999999999999888764

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

Probab=97.23  E-value=0.0071  Score=46.66  Aligned_cols=112  Identities=12%  Similarity=0.093  Sum_probs=69.2

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHh
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA   99 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~   99 (145)
                      -+-+.|--..+..+|++++.+.   ..+.| |....+-+-+.|-+.|+-.+|.+.+-.--  .-++.|..|-.=|..-|-
T Consensus       563 qianiye~led~aqaie~~~q~---~slip~dp~ilskl~dlydqegdksqafq~~ydsy--ryfp~nie~iewl~ayyi  637 (840)
T KOG2003|consen  563 QIANIYELLEDPAQAIELLMQA---NSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSY--RYFPCNIETIEWLAAYYI  637 (840)
T ss_pred             HHHHHHHHhhCHHHHHHHHHHh---cccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcc--cccCcchHHHHHHHHHHH
Confidence            3334444445555555555443   33444 56677777777888887777777655433  123334444333333332


Q ss_pred             cC----------------CCchhhHHHHHHHH-HhccChhHHHHHHccCCCCCCC
Q 047113          100 TG----------------ETEPYVWGALLGAC-RIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       100 ~~----------------~p~~~~~~~li~~~-~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ..                .|+..-|-.+|..| .+.|++.+|+.+++.+.+..|.
T Consensus       638 dtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpe  692 (840)
T KOG2003|consen  638 DTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPE  692 (840)
T ss_pred             hhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCcc
Confidence            22                88999999998777 4579999999999887775553

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.22  E-value=0.0095  Score=39.67  Aligned_cols=107  Identities=11%  Similarity=0.065  Sum_probs=71.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC--cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP--NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYG   92 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~   92 (145)
                      ...|..+...+...|++++|...|+.... ..-.|  ...++..+-..+...|++++|...++... .  +.|+ ..++.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~-l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al-~--~~~~~~~~~~  110 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMR-LEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQAL-E--RNPFLPQALN  110 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh-ccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCcCcHHHHH
Confidence            45788899999999999999999999865 32222  23578888899999999999999999988 3  2343 33333


Q ss_pred             HHHHHHhcCCCchhhHHHHHHHHHhccChh-------HHHHHHccCCCCCC
Q 047113           93 ITVDLLATGETEPYVWGALLGACRIHHNVK-------IGELVAKDPFHLDP  136 (145)
Q Consensus        93 ~li~~~~~~~p~~~~~~~li~~~~~~g~~~-------~a~~~~~~~~~~~~  136 (145)
                      .+...|.          .+-..+.+.|+++       +|..++++..+..|
T Consensus       111 ~la~i~~----------~~~~~~~~~g~~~~A~~~~~~a~~~~~~a~~~~p  151 (168)
T CHL00033        111 NMAVICH----------YRGEQAIEQGDSEIAEAWFDQAAEYWKQAIALAP  151 (168)
T ss_pred             HHHHHHH----------HhhHHHHHcccHHHHHHHHHHHHHHHHHHHHhCc
Confidence            3332222          1222333677766       44555555555555

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.21  E-value=0.0082  Score=41.96  Aligned_cols=62  Identities=13%  Similarity=0.101  Sum_probs=32.6

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH-HHHHHHHHHhhcc--------chHHHHHHHHHHhh
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN-VTFLSILFACSYS--------GLIEEGIKVFDIMV   79 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~-~~~~~ll~~~~~~--------~~~~~a~~~~~~m~   79 (145)
                      .|..+..++.+.|++++|...|+.+.+...-.|.. ..+..+-.++.+.        |+.+.|...++.+.
T Consensus        72 a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~  142 (235)
T TIGR03302        72 AQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELI  142 (235)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHH
Confidence            55666667777777777777777765411111111 1222222223322        56666777776666

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).

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

Probab=97.17  E-value=0.0071  Score=38.43  Aligned_cols=84  Identities=19%  Similarity=0.267  Sum_probs=66.1

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+-..+.+.|++++|...|++... .+ +.+...+..+-..+...|+++.|...|+..
T Consensus        34 ~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a  111 (135)
T TIGR02552        34 DEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAA-LD-PDDPRPYFHAAECLLALGEPESALKALDLA  111 (135)
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            46777777653   34678899999999999999999999998765 33 336778888888999999999999999988


Q ss_pred             hhhcCcCccHHH
Q 047113           79 VHDFQLDLNLEH   90 (145)
Q Consensus        79 ~~~~~~~~~~~~   90 (145)
                      . +  ..|+...
T Consensus       112 l-~--~~p~~~~  120 (135)
T TIGR02552       112 I-E--ICGENPE  120 (135)
T ss_pred             H-H--hccccch
Confidence            8 3  3454444

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

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

Probab=97.15  E-value=0.01  Score=41.79  Aligned_cols=117  Identities=12%  Similarity=0.018  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVD   96 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~   96 (145)
                      .--|-.+|.+.|++..|..-++...+ .  .| +..+|.++-..|.+.|+.+.|.+-|+...   .+.| +..+.|...-
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~-~--DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAl---sl~p~~GdVLNNYG~  111 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALE-H--DPSYYLAHLVRAHYYQKLGENDLADESYRKAL---SLAPNNGDVLNNYGA  111 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH-h--CcccHHHHHHHHHHHHHcCChhhHHHHHHHHH---hcCCCccchhhhhhH
Confidence            44556677777788888777777655 3  34 45577777777778888877777777766   2344 2333333333


Q ss_pred             HHhcC---------------CC----chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           97 LLATG---------------ET----EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        97 ~~~~~---------------~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      -+|..               .|    -..+|..+.-+..+.|+.+.|...+++..+.+|+.+..
T Consensus       112 FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~  175 (250)
T COG3063         112 FLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPA  175 (250)
T ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChH
Confidence            33333               22    23467777777788899999999999988888876653

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=97.14  E-value=0.0048  Score=43.89  Aligned_cols=104  Identities=13%  Similarity=0.114  Sum_probs=65.6

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      |..+ -.+=.++...|+-+.+..+......  .-.-|....+...+...+.|++..|...+++.. .  ..         
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~--~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~-~--l~---------  130 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAI--AYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAA-R--LA---------  130 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhc--cCcccHHHHHHHHHHHHHhcchHHHHHHHHHHh-c--cC---------
Confidence            4444 4555677778888888877776432  122355566778999999999999999999998 2  22         


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                             ++|+..|+.+--+|-+.|+++.|+.-+.+..++.|.++.
T Consensus       131 -------p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~  169 (257)
T COG5010         131 -------PTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPS  169 (257)
T ss_pred             -------CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCch
Confidence                   235555555555555555555555555555554444443

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.12  E-value=0.021  Score=37.88  Aligned_cols=94  Identities=12%  Similarity=-0.014  Sum_probs=67.8

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      ..=.+-.-+.+.|++++|..+|+....   +.| +..-|-.+--+|-..|++++|...+.... .  +.||         
T Consensus        37 ~lY~~A~~ly~~G~l~~A~~~f~~L~~---~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~-~--L~~d---------  101 (157)
T PRK15363         37 TLYRYAMQLMEVKEFAGAARLFQLLTI---YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAA-Q--IKID---------  101 (157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHH-h--cCCC---------
Confidence            333445566789999999999999866   456 55566777778888999999999999888 3  3343         


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                             |...+=.+-.++...|+.+.|+..|+....
T Consensus       102 -------dp~~~~~ag~c~L~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363        102 -------APQAPWAAAECYLACDNVCYAIKALKAVVR  131 (157)
T ss_pred             -------CchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                   445555556666777777777777776544

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.11  E-value=0.0031  Score=35.00  Aligned_cols=55  Identities=18%  Similarity=0.262  Sum_probs=46.8

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           22 MIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +-..+.+.|++++|...|++..+ ..  | +...+..+-.++.+.|++++|...|++..
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~-~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALK-QD--PDNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHC-CS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH-HC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34678899999999999999876 43  5 67788999999999999999999999987

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

Probab=97.06  E-value=0.00077  Score=39.69  Aligned_cols=73  Identities=18%  Similarity=0.201  Sum_probs=52.8

Q ss_pred             chHHHHhccCCC--C---chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K---NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~--~---~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|..+|+.+..  |   +...|-.+-.++.+.|++++|..+++. .. .+-. +....-.+-.++-+.|++++|..+++
T Consensus         6 ~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~-~~~~-~~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen    6 ENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LK-LDPS-NPDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             HHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HT-HHHC-HHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hC-CCCC-CHHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            568888887743  3   344566689999999999999999988 33 2222 32333355788999999999999987


Q ss_pred             H
Q 047113           77 I   77 (145)
Q Consensus        77 ~   77 (145)
                      +
T Consensus        83 ~   83 (84)
T PF12895_consen   83 K   83 (84)
T ss_dssp             H
T ss_pred             c
Confidence            5

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.04  E-value=0.0076  Score=49.11  Aligned_cols=105  Identities=9%  Similarity=-0.013  Sum_probs=84.9

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      ++..+-.|-.+..+.|+.++|..+++...+   +.|| ......+...+.+.+.+++|....++.. .  ..|+      
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~---~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l-~--~~p~------  152 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQ---RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYF-S--GGSS------  152 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHh---hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHh-h--cCCC------
Confidence            566788888889999999999999999855   6785 5577888899999999999999999888 3  2333      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                                +....+.+-.++...|++++|..+|+++....|+++..
T Consensus       153 ----------~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~~~~~  190 (694)
T PRK15179        153 ----------SAREILLEAKSWDEIGQSEQADACFERLSRQHPEFENG  190 (694)
T ss_pred             ----------CHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCcHHH
Confidence                      44555666788899999999999999998877765544

>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=97.03  E-value=0.0073  Score=33.83  Aligned_cols=62  Identities=26%  Similarity=0.316  Sum_probs=54.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc-hHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG-LIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~-~~~~a~~~~~~m~   79 (145)
                      +..+|..+-..+.+.|++++|+..|.+..+ .  .| +...|..+-.++.+.| ++++|...++...
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~-~--~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIE-L--DPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHH-H--STTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-c--CCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            457899999999999999999999999876 4  35 6778899999999999 8999999998876

...

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.99  E-value=0.019  Score=41.69  Aligned_cols=105  Identities=12%  Similarity=0.094  Sum_probs=77.9

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH-HHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV-TFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      |...|--|-.+|.+.|+++.|...|+.-.+..|=.|+.. -|...+-.-+......++..+|+++.   ..+|+      
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al---~~D~~------  225 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQAL---ALDPA------  225 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH---hcCCc------
Confidence            788999999999999999999999999866344444433 33333433344445668999999988   34443      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                                |..+-..|--++...|++.+|...|+.|.+..|.+
T Consensus       226 ----------~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~  260 (287)
T COG4235         226 ----------NIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPAD  260 (287)
T ss_pred             ----------cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCC
Confidence                      55555666788899999999999999999966543

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

Probab=96.97  E-value=0.011  Score=33.79  Aligned_cols=76  Identities=20%  Similarity=0.276  Sum_probs=60.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...|+...   +.+...|..+...+...|++++|...|..... .. +.+..++..+...+...|+++.|...+...
T Consensus        17 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~   94 (100)
T cd00189          17 DEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALE-LD-PDNAKAYYNLGLAYYKLGKYEEALEAYEKA   94 (100)
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CC-CcchhHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            56777777653   23456788899999999999999999998765 33 335568888888999999999999999887


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus        95 ~   95 (100)
T cd00189          95 L   95 (100)
T ss_pred             H
Confidence            6

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

Probab=96.96  E-value=0.034  Score=42.96  Aligned_cols=126  Identities=11%  Similarity=0.059  Sum_probs=103.5

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      |+|...|++..+   .-...|..|-.-|..-.....|.+.|++..+   +-| |-..|=.+-.+|.-.+.-.-|.-.|++
T Consensus       347 EKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvd---i~p~DyRAWYGLGQaYeim~Mh~YaLyYfqk  423 (559)
T KOG1155|consen  347 EKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVD---INPRDYRAWYGLGQAYEIMKMHFYALYYFQK  423 (559)
T ss_pred             HHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHh---cCchhHHHHhhhhHHHHHhcchHHHHHHHHH
Confidence            678888886543   3466899999999999999999999999765   445 778888899999888888888888888


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..   .+.| |...|.+|.++|.+.                 ..+...+..|-+.|-+.++.++|...+++-.+
T Consensus       424 A~---~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  424 AL---ELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HH---hcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            87   4666 689999999999877                 44557888899999999999999998887544

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=96.96  E-value=0.013  Score=44.00  Aligned_cols=88  Identities=14%  Similarity=0.095  Sum_probs=68.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|++.-   +.+...|..+-.++.+.|++++|+..+++...   +.| +...|..+-.++...|+++.|...|+.
T Consensus        19 ~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~---l~P~~~~a~~~lg~~~~~lg~~~eA~~~~~~   95 (356)
T PLN03088         19 ALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIE---LDPSLAKAYLRKGTACMKLEEYQTAKAALEK   95 (356)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcCCHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            46777777553   34677899999999999999999999999876   345 677888888999999999999999999


Q ss_pred             hhhhcCcCccHHHHHHHH
Q 047113           78 MVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li   95 (145)
                      .. .  +.|+-.....++
T Consensus        96 al-~--l~P~~~~~~~~l  110 (356)
T PLN03088         96 GA-S--LAPGDSRFTKLI  110 (356)
T ss_pred             HH-H--hCCCCHHHHHHH
Confidence            98 3  455433333333

>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=96.94  E-value=0.0024  Score=35.90  Aligned_cols=67  Identities=21%  Similarity=0.162  Sum_probs=54.9

Q ss_pred             cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhcc-ChhHHHHHHc
Q 047113           51 NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHH-NVKIGELVAK  129 (145)
Q Consensus        51 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~  129 (145)
                      +...|..+-..+.+.|+++.|...|++.. +  +.|+                +...|..+-.+|...| ++++|+..++
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai-~--~~p~----------------~~~~~~~~g~~~~~~~~~~~~A~~~~~   62 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAI-E--LDPN----------------NAEAYYNLGLAYMKLGKDYEEAIEDFE   62 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHH-H--HSTT----------------HHHHHHHHHHHHHHTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--cCCC----------------CHHHHHHHHHHHHHhCccHHHHHHHHH
Confidence            46678888889999999999999999998 3  3343                5567777888899999 7999999998


Q ss_pred             cCCCCCC
Q 047113          130 DPFHLDP  136 (145)
Q Consensus       130 ~~~~~~~  136 (145)
                      +..+++|
T Consensus        63 ~al~l~P   69 (69)
T PF13414_consen   63 KALKLDP   69 (69)
T ss_dssp             HHHHHST
T ss_pred             HHHHcCc
Confidence            8776655

...

>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=96.90  E-value=0.0053  Score=44.85  Aligned_cols=121  Identities=6%  Similarity=-0.027  Sum_probs=84.9

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHH---HHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTF---LSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEH   90 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~---~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   90 (145)
                      .+.......+..+.+.+|++.|.+.++.|++ .  -.|....   .+.+........+..|..+|+++. + .+.+++.+
T Consensus       129 ~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~-~--~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~-~-~~~~t~~~  203 (290)
T PF04733_consen  129 GSLELLALAVQILLKMNRPDLAEKELKNMQQ-I--DEDSILTQLAEAWVNLATGGEKYQDAFYIFEELS-D-KFGSTPKL  203 (290)
T ss_dssp             TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHC-C--SCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHH-C-CS--SHHH
T ss_pred             CcccHHHHHHHHHHHcCCHHHHHHHHHHHHh-c--CCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHH-h-ccCCCHHH
Confidence            4566777888999999999999999999976 3  3444332   333444444457999999999997 3 45677777


Q ss_pred             HHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccCh-hHHHHHHccCCCCCCCCC
Q 047113           91 YGITVDLLATG-----------------ETEPYVWGALLGACRIHHNV-KIGELVAKDPFHLDPKND  139 (145)
Q Consensus        91 ~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~-~~a~~~~~~~~~~~~~~~  139 (145)
                      .+.+.-+....                 +.|..+...++-...-.|+. +.+.+.+..++...|+.|
T Consensus       204 lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~~p~h~  270 (290)
T PF04733_consen  204 LNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQSNPNHP  270 (290)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHHTTTSH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHhCCCCh
Confidence            77666555544                 44666777787777778887 778889999888877543

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.

>TIGR00540 hemY_coli hemY protein

Probab=96.88  E-value=0.047  Score=41.71  Aligned_cols=116  Identities=9%  Similarity=-0.039  Sum_probs=80.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHH---HHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVT---FLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHY   91 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~---~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   91 (145)
                      +...+-.+...+.+.|++++|.+++++..+   ..||...   .....-.....++.+.+...++...+...-.|+....
T Consensus       262 ~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~---~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll  338 (409)
T TIGR00540       262 NIALKIALAEHLIDCDDHDSAQEIIFDGLK---KLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCIN  338 (409)
T ss_pred             CHHHHHHHHHHHHHCCChHHHHHHHHHHHh---hCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHH
Confidence            777888999999999999999999999755   3455442   1222222344567778888887776333333322444


Q ss_pred             HHHHHHHhcC------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           92 GITVDLLATG------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        92 ~~li~~~~~~------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .++...+.+.                  .|+...+..+...+...|+.++|.+++++...
T Consensus       339 ~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       339 RALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4555555543                  68888888888999999999999999887543

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.

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.82  E-value=0.073  Score=42.10  Aligned_cols=126  Identities=12%  Similarity=0.086  Sum_probs=81.8

Q ss_pred             CchhhHHHHHHHHHHcC-----ChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhcc--------chHHHHHHHHHHhh
Q 047113           14 KNVVIWSGMIASHAIHG-----QEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYS--------GLIEEGIKVFDIMV   79 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g-----~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~--------~~~~~a~~~~~~m~   79 (145)
                      .|...|...+.|.....     ..++|..+|++..+   ..|+ ...|..+..++...        .+++.+.+......
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~---ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILK---SEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            47788999998866533     37799999999866   4575 44555443333221        22334444444333


Q ss_pred             hhcCcCccHHHHHHHHHH--HhcC--------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           80 HDFQLDLNLEHYGITVDL--LATG--------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~--~~~~--------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      .......+...|.++.-.  +...              .|+...|..+-+.+...|+.++|.+.+++..+++|..|++|
T Consensus       412 al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt~~  490 (517)
T PRK10153        412 ALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENTLY  490 (517)
T ss_pred             hcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCchHH
Confidence            111122344555544322  2222              77888999999999999999999999999999999887654

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

Probab=96.80  E-value=0.044  Score=40.56  Aligned_cols=97  Identities=12%  Similarity=0.002  Sum_probs=54.7

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhc
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  100 (145)
                      .+-..+...|++++|...+++..+ .. +.+...+..+-..+.+.|++++|...++... ..  .|.             
T Consensus       119 ~~a~~~~~~G~~~~A~~~~~~al~-~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l-~~--~~~-------------  180 (355)
T cd05804         119 MLAFGLEEAGQYDRAEEAARRALE-LN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWR-DT--WDC-------------  180 (355)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh-hC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhh-hc--cCC-------------
Confidence            333455555666666666655543 21 1133344555555555666666665555554 11  110             


Q ss_pred             CCCch--hhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113          101 GETEP--YVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       101 ~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                       .|+.  ..|..+...+...|++++|..++++.....|
T Consensus       181 -~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~  217 (355)
T cd05804         181 -SSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSA  217 (355)
T ss_pred             -CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhcccc
Confidence             1222  2455677888999999999999998765444

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.

>PLN02789 farnesyltranstransferase

Probab=96.78  E-value=0.033  Score=41.36  Aligned_cols=121  Identities=13%  Similarity=0.025  Sum_probs=86.6

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc-hHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG-LIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      .+++.+-..+...++.++|+.++....+   +.| +...|+.--.+....| .++++...++.+. ..+ .-+...|+.-
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~---lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i-~~n-pknyqaW~~R  112 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIR---LNPGNYTVWHFRRLCLEALDADLEEELDFAEDVA-EDN-PKNYQIWHHR  112 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHH---HCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHH-HHC-CcchHHhHHH
Confidence            3577777888888999999999999876   456 3446665555556666 5788888888877 322 2234445422


Q ss_pred             ---HHHHhc------------C----CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           95 ---VDLLAT------------G----ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        95 ---i~~~~~------------~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                         +..+.+            .    +.+..+|+...-++...|+++++++.++++.+.+|.+.+.|
T Consensus       113 ~~~l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW  179 (320)
T PLN02789        113 RWLAEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAW  179 (320)
T ss_pred             HHHHHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHH
Confidence               222211            1    55778999999999999999999999999999888776654

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.71  E-value=0.029  Score=40.45  Aligned_cols=104  Identities=12%  Similarity=0.055  Sum_probs=74.5

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH----HHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN----VTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      ..|+..+....+.|++++|...|+.+..   .-|+.    ..+--+-.++-..|+++.|...|+.+..++.-  +...  
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~---~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~--s~~~--  216 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVK---KYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPK--SPKA--  216 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH---HCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC--Ccch--
Confidence            3577777777778999999999999865   23432    35556667788999999999999999843221  1112  


Q ss_pred             HHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           93 ITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        93 ~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                                  ...+-.+...+...|+.++|..+++.+.+..|+..
T Consensus       217 ------------~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~s~  251 (263)
T PRK10803        217 ------------ADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPGTD  251 (263)
T ss_pred             ------------hHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCH
Confidence                        22233345667788999999999998888777543

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=96.68  E-value=0.0093  Score=41.09  Aligned_cols=94  Identities=10%  Similarity=0.052  Sum_probs=63.1

Q ss_pred             CChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHH
Q 047113           30 GQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWG  109 (145)
Q Consensus        30 g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~  109 (145)
                      ++.+++...++...+ .. +.|...|..+-..+...|+++.|...+++.. +  +.|+                +...+.
T Consensus        53 ~~~~~~i~~l~~~L~-~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al-~--l~P~----------------~~~~~~  111 (198)
T PRK10370         53 QTPEAQLQALQDKIR-AN-PQNSEQWALLGEYYLWRNDYDNALLAYRQAL-Q--LRGE----------------NAELYA  111 (198)
T ss_pred             hhHHHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H--hCCC----------------CHHHHH
Confidence            344555555555433 11 2366777777778888888888888887776 2  3332                555666


Q ss_pred             HHHHHH-HhccC--hhHHHHHHccCCCCCCCCCCCccc
Q 047113          110 ALLGAC-RIHHN--VKIGELVAKDPFHLDPKNDAYYTS  144 (145)
Q Consensus       110 ~li~~~-~~~g~--~~~a~~~~~~~~~~~~~~~~~~~~  144 (145)
                      .+-.++ ...|+  .++|..++++..+.+|+++..+.+
T Consensus       112 ~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al~~  149 (198)
T PRK10370        112 ALATVLYYQAGQHMTPQTREMIDKALALDANEVTALML  149 (198)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHHHH
Confidence            666653 56676  599999999999999988766543

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

Probab=96.66  E-value=0.0091  Score=42.85  Aligned_cols=108  Identities=12%  Similarity=-0.049  Sum_probs=78.5

Q ss_pred             HHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-
Q 047113           23 IASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-  101 (145)
Q Consensus        23 i~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-  101 (145)
                      ...|+..|++++|++..+.-       -+......=+....+...+|.|+.-++.|. +-   -+-.|.+-|.+++.+. 
T Consensus       115 a~i~~~~~~~deAl~~~~~~-------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq-~i---ded~tLtQLA~awv~la  183 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHLG-------ENLEAAALNVQILLKMHRFDLAEKELKKMQ-QI---DEDATLTQLAQAWVKLA  183 (299)
T ss_pred             hHHhhcCCChHHHHHHHhcc-------chHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cc---chHHHHHHHHHHHHHHh
Confidence            34577899999999998762       133333333444677888999999999998 31   1345555555555544 


Q ss_pred             --------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          102 --------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       102 --------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                                          +|...+-|...-++...|++++|..+.+......+++|.+
T Consensus       184 ~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpet  243 (299)
T KOG3081|consen  184 TGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPET  243 (299)
T ss_pred             ccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHH
Confidence                                7888888888889999999999999999988777666544

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.66  E-value=0.0084  Score=49.96  Aligned_cols=119  Identities=12%  Similarity=-0.030  Sum_probs=86.8

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc------------C
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF------------Q   83 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~------------~   83 (145)
                      ..|..|-..|+..-++..|.++|+...+   +.| |........+.+++..+++.|..+.-....+.            |
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFe---LDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG  569 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFE---LDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRG  569 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhc---CCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhcc
Confidence            4788999999888899999999998755   444 77799999999999999999999843332111            1


Q ss_pred             -cCccHHHHHHHHH----HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           84 -LDLNLEHYGITVD----LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        84 -~~~~~~~~~~li~----~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                       ..|...-..-.|-    ++.-.+.|...|..+..+|.+.|++..|+.+|.+...++|.+
T Consensus       570 ~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s  629 (1238)
T KOG1127|consen  570 PYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLS  629 (1238)
T ss_pred             ccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHh
Confidence             0122222221111    111115588899999999999999999999999999888854

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

Probab=96.63  E-value=0.06  Score=41.91  Aligned_cols=132  Identities=10%  Similarity=0.011  Sum_probs=88.6

Q ss_pred             chHHHHhc-cCC-CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            2 DDAERIFG-GII-DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         2 ~~A~~~f~-~m~-~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ..|..+|+ .|. +||...|++.|+-=.+-..++.|..+|.....   +.|++.+|.--..---+.|++..+..+++...
T Consensus       158 ~gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~---~HP~v~~wikyarFE~k~g~~~~aR~VyerAi  234 (677)
T KOG1915|consen  158 AGARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVL---VHPKVSNWIKYARFEEKHGNVALARSVYERAI  234 (677)
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe---ecccHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            34667776 342 58888888888888888888888888888754   56888888877777777888877777777666


Q ss_pred             hhcCcC-ccHHHHHHHHHHHhcC---------------------------------------------------------
Q 047113           80 HDFQLD-LNLEHYGITVDLLATG---------------------------------------------------------  101 (145)
Q Consensus        80 ~~~~~~-~~~~~~~~li~~~~~~---------------------------------------------------------  101 (145)
                      ...|-+ .+...+.++..-=.++                                                         
T Consensus       235 e~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~  314 (677)
T KOG1915|consen  235 EFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKE  314 (677)
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHH
Confidence            322211 1111222211100010                                                         


Q ss_pred             ----CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113          102 ----ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       102 ----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                          +.|..+|--.+.--...|+.+...+++++.....|
T Consensus       315 v~~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvp  353 (677)
T KOG1915|consen  315 VSKNPYNYDSWFDYLRLEESVGDKDRIRETYERAIANVP  353 (677)
T ss_pred             HHhCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCC
Confidence                45667888888888888999999999988766433

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=96.63  E-value=0.014  Score=45.75  Aligned_cols=105  Identities=9%  Similarity=0.066  Sum_probs=78.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhh----cC-CCCcHHHH-HHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHC----SD-GKPNNVTF-LSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEH   90 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~----~~-~~p~~~~~-~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   90 (145)
                      .+...|-..|...|+++.|..++.+..+.    .| ..|...+. +.+-..+...+.+++|..+|+++..          
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~----------  269 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALT----------  269 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH----------
Confidence            45666999999999999999999987551    12 24454433 4577788889999999999998872          


Q ss_pred             HHHHHHHHhcCCCch-hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           91 YGITVDLLATGETEP-YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        91 ~~~li~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                        .....|++..|.+ .+++.|-..|.+.|++++|...+++..+
T Consensus       270 --i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~  311 (508)
T KOG1840|consen  270 --IREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALE  311 (508)
T ss_pred             --HHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHH
Confidence              3444555554433 5777888899999999999998887655

>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=96.61  E-value=0.0081  Score=34.56  Aligned_cols=63  Identities=14%  Similarity=0.134  Sum_probs=50.5

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhh-cCCC---Cc-HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHC-SDGK---PN-NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~-~~~~---p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .+|+.+-..|.+.|++++|+..|++.... ..+.   |+ ..+++.+-..+...|++++|.+.+++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            47999999999999999999999986531 1122   33 5688899999999999999999998765

...

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.52  E-value=0.00084  Score=34.62  Aligned_cols=37  Identities=24%  Similarity=0.345  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCcc
Q 047113          107 VWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYT  143 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  143 (145)
                      +|..+-.+|.+.|++++|.+++++..+..|+++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~   39 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWR   39 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHH
Confidence            5777889999999999999999999999998876554

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.44  E-value=0.18  Score=35.21  Aligned_cols=125  Identities=12%  Similarity=-0.070  Sum_probs=82.7

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccH-HHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNL-EHYG   92 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~   92 (145)
                      ....+-.+...+.+.|++++|...|++......-.|. ...+..+-.++-..|+++.|...++.+.....-.|.. .++.
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            4567888888999999999999999998651211121 2466778888999999999999999998333222221 1233


Q ss_pred             HHHHHHhc---------------------C---CCch-hhHH-----------------HHHHHHHhccChhHHHHHHcc
Q 047113           93 ITVDLLAT---------------------G---ETEP-YVWG-----------------ALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        93 ~li~~~~~---------------------~---~p~~-~~~~-----------------~li~~~~~~g~~~~a~~~~~~  130 (145)
                      .+..++.+                     .   .|+. ..+.                 .+-..|.+.|++++|...++.
T Consensus       112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~  191 (235)
T TIGR03302       112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFET  191 (235)
T ss_pred             HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            33333321                     1   3433 2221                 234567788999999999999


Q ss_pred             CCCCCCCCC
Q 047113          131 PFHLDPKND  139 (145)
Q Consensus       131 ~~~~~~~~~  139 (145)
                      ..+..|+.+
T Consensus       192 al~~~p~~~  200 (235)
T TIGR03302       192 VVENYPDTP  200 (235)
T ss_pred             HHHHCCCCc
Confidence            888766543

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).

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.42  E-value=0.031  Score=37.09  Aligned_cols=84  Identities=12%  Similarity=-0.016  Sum_probs=67.4

Q ss_pred             CchHHHHhccCCC--C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            1 MDDAERIFGGIID--K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         1 ~~~A~~~f~~m~~--~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      +++|+++|+.+..  | +..-|-.|-..+-+.|++++|+..|..... .+ +-|...+-.+-.++-..|+.+.|+..|+.
T Consensus        51 l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~-L~-~ddp~~~~~ag~c~L~lG~~~~A~~aF~~  128 (157)
T PRK15363         51 FAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQ-IK-IDAPQAPWAAAECYLACDNVCYAIKALKA  128 (157)
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-cC-CCCchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            3689999996642  3 566788899999999999999999999876 44 23678888888899999999999999998


Q ss_pred             hhhhcCcCc
Q 047113           78 MVHDFQLDL   86 (145)
Q Consensus        78 m~~~~~~~~   86 (145)
                      .....+-.|
T Consensus       129 Ai~~~~~~~  137 (157)
T PRK15363        129 VVRICGEVS  137 (157)
T ss_pred             HHHHhccCh
Confidence            884444333

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

Probab=96.42  E-value=0.069  Score=41.63  Aligned_cols=125  Identities=10%  Similarity=0.075  Sum_probs=89.5

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+=|+...+   .++..|--+--+..|.+++++++..|.+.++  .++.....||..-......++++.|..-|+..
T Consensus       411 e~A~aDF~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kk--kFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~a  488 (606)
T KOG0547|consen  411 EEAIADFQKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKK--KFPNCPEVYNLFAEILTDQQQFDKAVKQYDKA  488 (606)
T ss_pred             HHHHHHHHHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCCCchHHHHHHHHHhhHHhHHHHHHHHHHH
Confidence            456666765433   3566777777888899999999999999864  56667889999999999999999999999987


Q ss_pred             hhhcCcCcc-------H--------------HHHHHHHHHHhcC---CCch-hhHHHHHHHHHhccChhHHHHHHccC
Q 047113           79 VHDFQLDLN-------L--------------EHYGITVDLLATG---ETEP-YVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        79 ~~~~~~~~~-------~--------------~~~~~li~~~~~~---~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      . +  ++|+       .              .-++.-++.+.+.   .|-. ..|-+|-..-...|+.++|.++|++.
T Consensus       489 i-~--LE~~~~~~~v~~~plV~Ka~l~~qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEks  563 (606)
T KOG0547|consen  489 I-E--LEPREHLIIVNAAPLVHKALLVLQWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKS  563 (606)
T ss_pred             H-h--hccccccccccchhhhhhhHhhhchhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            7 2  2332       1              1122222333333   4433 46788888888889999999999863

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=96.40  E-value=0.13  Score=33.33  Aligned_cols=24  Identities=4%  Similarity=-0.161  Sum_probs=19.1

Q ss_pred             hHHHHHHHHHhccChhHHHHHHcc
Q 047113          107 VWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      .+...-+.|.+.|+.++|+..|+.
T Consensus       120 ~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  120 AAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHH
Confidence            445566888999999999998875

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

Probab=96.35  E-value=0.19  Score=38.00  Aligned_cols=112  Identities=15%  Similarity=0.047  Sum_probs=84.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ++..=.+++.-+.+-|+.++|.++..+-.+ .+..|.    -..+-.+.+.++...-+...+.-..+.+-.|  ..+.+|
T Consensus       262 ~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk-~~~D~~----L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tL  334 (400)
T COG3071         262 DPELVVAYAERLIRLGDHDEAQEIIEDALK-RQWDPR----LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTL  334 (400)
T ss_pred             ChhHHHHHHHHHHHcCChHHHHHHHHHHHH-hccChh----HHHHHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHH
Confidence            566666788888899999999999988766 666665    2333455666776665665555554555555  667777


Q ss_pred             HHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           95 VDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        95 i~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ...|.+.                .|+..+|+.+-+++.+.|+.++|.+..++...
T Consensus       335 G~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~  389 (400)
T COG3071         335 GRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALL  389 (400)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            7777776                89999999999999999999999999988544

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

Probab=96.30  E-value=0.08  Score=43.73  Aligned_cols=113  Identities=15%  Similarity=0.148  Sum_probs=56.6

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+++.++-.   .+...|-+|-..|-+.|+.++++..+-....   +.| |..-|..+-+...+.|++++|.-.|.+
T Consensus       156 eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAH---L~p~d~e~W~~ladls~~~~~i~qA~~cy~r  232 (895)
T KOG2076|consen  156 EEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAH---LNPKDYELWKRLADLSEQLGNINQARYCYSR  232 (895)
T ss_pred             HHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHh---cCCCChHHHHHHHHHHHhcccHHHHHHHHHH
Confidence            344445444421   2344455555555555555555555443322   222 444555555555555555555555555


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .. +..                  ++++..+---+.-|-+.|+...|...|.++....|
T Consensus       233 AI-~~~------------------p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p  272 (895)
T KOG2076|consen  233 AI-QAN------------------PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDP  272 (895)
T ss_pred             HH-hcC------------------CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC
Confidence            54 211                  33444444445556666666666666666666544

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

Probab=96.30  E-value=0.073  Score=38.67  Aligned_cols=30  Identities=17%  Similarity=0.193  Sum_probs=18.7

Q ss_pred             hHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113          107 VWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .|...++-=.+.|+++.+..+.+++.+.-|
T Consensus       109 iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~  138 (280)
T PF05843_consen  109 IWKKFIEFESKYGDLESVRKVEKRAEELFP  138 (280)
T ss_dssp             HHHHHHHHHHHHS-HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhh
Confidence            566666666666777777777766666444

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.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.25  E-value=0.038  Score=42.58  Aligned_cols=62  Identities=13%  Similarity=0.125  Sum_probs=55.1

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH----HHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN----VTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +...|+.+-.+|.+.|++++|+..|++-.+   +.|+.    .+|..+--++...|++++|.+.+++..
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALe---L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrAL  139 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALE---LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTAL  139 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            567899999999999999999999999755   56764    358999999999999999999999988

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=96.23  E-value=0.12  Score=40.07  Aligned_cols=101  Identities=20%  Similarity=0.113  Sum_probs=78.7

Q ss_pred             HHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHHHHHhcC-
Q 047113           25 SHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITVDLLATG-  101 (145)
Q Consensus        25 a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~-  101 (145)
                      .+.+.|.+++|+..++.+..   -.|| ..-+....+.+.+.++.++|.+.++.+.   ...|+ ...+-.+.++|.+. 
T Consensus       315 ~~~~~~~~d~A~~~l~~L~~---~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal---~l~P~~~~l~~~~a~all~~g  388 (484)
T COG4783         315 QTYLAGQYDEALKLLQPLIA---AQPDNPYYLELAGDILLEANKAKEAIERLKKAL---ALDPNSPLLQLNLAQALLKGG  388 (484)
T ss_pred             HHHHhcccchHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHH---hcCCCccHHHHHHHHHHHhcC
Confidence            45578999999999999754   4565 4555777888999999999999999998   34665 55566666666665 


Q ss_pred             ----------------CCchhhHHHHHHHHHhccChhHHHHHHccC
Q 047113          102 ----------------ETEPYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus       102 ----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                                      +-|...|..|-.+|...|+..++.....+.
T Consensus       389 ~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         389 KPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             ChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence                            446789999999999999998888766553

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

Probab=96.22  E-value=0.009  Score=44.31  Aligned_cols=127  Identities=9%  Similarity=0.015  Sum_probs=75.9

Q ss_pred             hHHHHhccCC--CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113            3 DAERIFGGII--DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus         3 ~A~~~f~~m~--~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      +|++.|+.-.  .|-+.||-.|-.+|.+..+++.|+.+|.+-..  .++.|+....-+-..+-..++.+.+.++++...+
T Consensus       241 ~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld--~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk  318 (478)
T KOG1129|consen  241 RAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLD--SFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLK  318 (478)
T ss_pred             hhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhh--cCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHh
Confidence            4666666432  35677888888888888888888888877532  2233444445566666677788888888887773


Q ss_pred             hcCcCccHHHHHHHH-------------HHHhcC----CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           81 DFQLDLNLEHYGITV-------------DLLATG----ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        81 ~~~~~~~~~~~~~li-------------~~~~~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ...+  ++..-.++.             .-|.+.    ..+..-|+.+--.|.-.+++|-++--|.+...
T Consensus       319 ~~~~--nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~RAls  386 (478)
T KOG1129|consen  319 LHPI--NVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQRALS  386 (478)
T ss_pred             cCCc--cceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHHHHHh
Confidence            2211  111111111             111111    44556667777777777777777777777554

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.19  E-value=0.053  Score=33.20  Aligned_cols=78  Identities=15%  Similarity=0.142  Sum_probs=59.4

Q ss_pred             chHHHHhccCCC--Cc----hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID--KN----VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~----~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.+.|+.+..  |+    ...+..+..++.+.|++++|...|+.......-.| ....+..+..++.+.|+++.|...
T Consensus        19 ~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~   98 (119)
T TIGR02795        19 ADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKAT   98 (119)
T ss_pred             HHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHH
Confidence            467788877643  32    34677789999999999999999999865121111 245677777888999999999999


Q ss_pred             HHHhh
Q 047113           75 FDIMV   79 (145)
Q Consensus        75 ~~~m~   79 (145)
                      ++.+.
T Consensus        99 ~~~~~  103 (119)
T TIGR02795        99 LQQVI  103 (119)
T ss_pred             HHHHH
Confidence            99998

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.

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.18  E-value=0.0099  Score=33.64  Aligned_cols=62  Identities=15%  Similarity=0.152  Sum_probs=50.3

Q ss_pred             HHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           60 FACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ..+.+.++++.|..+++.+. .  +.|+                +...|...-..+...|++++|.+.+++..+..|+++
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l-~--~~p~----------------~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~   63 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERAL-E--LDPD----------------DPELWLQRARCLFQLGRYEEALEDLERALELSPDDP   63 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHH-H--hCcc----------------cchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcH
Confidence            45788899999999999998 3  3333                556677778888999999999999999999888765


Q ss_pred             C
Q 047113          140 A  140 (145)
Q Consensus       140 ~  140 (145)
                      .
T Consensus        64 ~   64 (73)
T PF13371_consen   64 D   64 (73)
T ss_pred             H
Confidence            4

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

Probab=96.16  E-value=0.086  Score=41.70  Aligned_cols=139  Identities=12%  Similarity=0.150  Sum_probs=83.8

Q ss_pred             chHHHHhccCCC--Cchh-hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHH-HHHHHHhhc-----cchHHHHH
Q 047113            2 DDAERIFGGIID--KNVV-IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTF-LSILFACSY-----SGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~~-~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~-~~ll~~~~~-----~~~~~~a~   72 (145)
                      ++|.+.++.-..  .|.. ..-..-..+.+.|+.++|..+|+.+.. .+  |+...| ..+..+.+-     ..+.+...
T Consensus        21 ~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~-rN--Pdn~~Yy~~L~~~~g~~~~~~~~~~~~~~   97 (517)
T PF12569_consen   21 EEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELID-RN--PDNYDYYRGLEEALGLQLQLSDEDVEKLL   97 (517)
T ss_pred             HHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HC--CCcHHHHHHHHHHHhhhcccccccHHHHH
Confidence            456666665443  3544 455666788899999999999999977 55  665555 444444422     22455566


Q ss_pred             HHHHHhhhhcC-------cCc---cHHHHHHHHHHHhcC-----------------------------------------
Q 047113           73 KVFDIMVHDFQ-------LDL---NLEHYGITVDLLATG-----------------------------------------  101 (145)
Q Consensus        73 ~~~~~m~~~~~-------~~~---~~~~~~~li~~~~~~-----------------------------------------  101 (145)
                      ++++.+...+-       +..   +..-|...++.|.+.                                         
T Consensus        98 ~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~  177 (517)
T PF12569_consen   98 ELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNG  177 (517)
T ss_pred             HHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccC
Confidence            66666542210       000   111222222222222                                         


Q ss_pred             -----------CCchhhH--HHHHHHHHhccChhHHHHHHccCCCCCCCCCCCcc
Q 047113          102 -----------ETEPYVW--GALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYT  143 (145)
Q Consensus       102 -----------~p~~~~~--~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  143 (145)
                                 .|....|  ..+-..|-..|++++|+..+++..+..|..+..|+
T Consensus       178 ~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~  232 (517)
T PF12569_consen  178 SFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYM  232 (517)
T ss_pred             CCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence                       2444445  45567788899999999999999998887665553

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 [], [].

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.13  E-value=0.048  Score=30.71  Aligned_cols=54  Identities=17%  Similarity=0.094  Sum_probs=46.3

Q ss_pred             HHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           23 IASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        23 i~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      -..|.+.+++++|.++++.+..   +.| +...+...-..+.+.|+++.|.+.++...
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~---~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l   56 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALE---LDPDDPELWLQRARCLFQLGRYEEALEDLERAL   56 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHH---hCcccchhhHHHHHHHHHhccHHHHHHHHHHHH
Confidence            3578899999999999999976   345 56677778888999999999999999998

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

Probab=96.12  E-value=0.067  Score=38.87  Aligned_cols=98  Identities=9%  Similarity=0.087  Sum_probs=70.7

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      .+|-.+|...-|.+..++|..+|.+.++......+.....+.|.-+ ..++.+.|..+|+...+..+             
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~-~~~d~~~A~~Ife~glk~f~-------------   67 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKKFP-------------   67 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHHHT-------------
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHHCC-------------
Confidence            5799999999999999999999999976223344555555555433 35667789999999884322             


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                            .+...|...++-....|+.+.|+.+|++....
T Consensus        68 ------~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~   99 (280)
T PF05843_consen   68 ------SDPDFWLEYLDFLIKLNDINNARALFERAISS   99 (280)
T ss_dssp             ------T-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCT
T ss_pred             ------CCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHh
Confidence                  25556777777888899999999999986653

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.

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

Probab=96.09  E-value=0.018  Score=45.27  Aligned_cols=38  Identities=11%  Similarity=0.032  Sum_probs=28.8

Q ss_pred             CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113          102 ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       102 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      +.|+.++.++--.|...|+++.|...|.+...+.|++.
T Consensus       486 ~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~  523 (611)
T KOG1173|consen  486 PKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNI  523 (611)
T ss_pred             CCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccH
Confidence            44667777777778888888888888888777777663

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

Probab=95.96  E-value=0.13  Score=38.15  Aligned_cols=111  Identities=13%  Similarity=0.048  Sum_probs=65.4

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHH---HHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHH
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLS---ILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITV   95 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~---ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li   95 (145)
                      .....+...|++++|...+++..+ .  .| |...++.   ........+..+.+.+.+...   ....|+ ......+.
T Consensus        48 ~~a~~~~~~g~~~~A~~~~~~~l~-~--~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~~~~~~a  121 (355)
T cd05804          48 VEALSAWIAGDLPKALALLEQLLD-D--YPRDLLALKLHLGAFGLGDFSGMRDHVARVLPLW---APENPDYWYLLGMLA  121 (355)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH-H--CCCcHHHHHHhHHHHHhcccccCchhHHHHHhcc---CcCCCCcHHHHHHHH
Confidence            334456678899999998888765 2  34 4444442   222222244455555554431   122333 22222322


Q ss_pred             HHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           96 DLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        96 ~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ..+...                 +.+...+..+-.++...|++++|...+++..+..|.
T Consensus       122 ~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~  180 (355)
T cd05804         122 FGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC  180 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC
Confidence            333322                 445567888889999999999999999998876654

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.

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=95.91  E-value=0.089  Score=42.69  Aligned_cols=117  Identities=15%  Similarity=0.145  Sum_probs=84.6

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhh--cCc---CccHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHD--FQL---DLNLEH   90 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--~~~---~~~~~~   90 (145)
                      ..-|.-.|..|+..|+..+|..+..+-.+   -+||...|..+.+.-.....++.|.++++..-.+  ..+   .-+-..
T Consensus       424 lemw~~vi~CY~~lg~~~kaeei~~q~le---k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~  500 (777)
T KOG1128|consen  424 LEMWDPVILCYLLLGQHGKAEEINRQELE---KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKD  500 (777)
T ss_pred             HHHHHHHHHHHHHhcccchHHHHHHHHhc---CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchh
Confidence            34588889999999999999999887543   4689999999999999999998888888765422  110   001111


Q ss_pred             HHHHHHHHhcC-------------------------------------CCc-hhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           91 YGITVDLLATG-------------------------------------ETE-PYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        91 ~~~li~~~~~~-------------------------------------~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      |.....-+-+.                                     .|| ..+||++-.+|.+.|+..+|...+.+..
T Consensus       501 fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAl  580 (777)
T KOG1128|consen  501 FSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEAL  580 (777)
T ss_pred             HHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHh
Confidence            22222111111                                     554 5799999999999999999999999988


Q ss_pred             CCC
Q 047113          133 HLD  135 (145)
Q Consensus       133 ~~~  135 (145)
                      +.+
T Consensus       581 Kcn  583 (777)
T KOG1128|consen  581 KCN  583 (777)
T ss_pred             hcC
Confidence            755

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

Probab=95.88  E-value=0.076  Score=41.89  Aligned_cols=79  Identities=14%  Similarity=0.120  Sum_probs=66.8

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .+|+.|-.+|.+.+++++|+..|+.-..   ..| |..+++++--.+...|+++.|...|.+..   .+.|+-.+-..++
T Consensus       456 p~~~NLGH~~Rkl~~~~eAI~~~q~aL~---l~~k~~~~~asig~iy~llgnld~Aid~fhKaL---~l~p~n~~~~~lL  529 (611)
T KOG1173|consen  456 PTLNNLGHAYRKLNKYEEAIDYYQKALL---LSPKDASTHASIGYIYHLLGNLDKAIDHFHKAL---ALKPDNIFISELL  529 (611)
T ss_pred             HHHHhHHHHHHHHhhHHHHHHHHHHHHH---cCCCchhHHHHHHHHHHHhcChHHHHHHHHHHH---hcCCccHHHHHHH
Confidence            4699999999999999999999998754   334 88899999999999999999999999888   7888877777776


Q ss_pred             HHHhcC
Q 047113           96 DLLATG  101 (145)
Q Consensus        96 ~~~~~~  101 (145)
                      ..+...
T Consensus       530 ~~aie~  535 (611)
T KOG1173|consen  530 KLAIED  535 (611)
T ss_pred             HHHHHh
Confidence            655443

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

Probab=95.81  E-value=0.047  Score=39.33  Aligned_cols=78  Identities=12%  Similarity=0.077  Sum_probs=60.8

Q ss_pred             chHHHHhccCCCC-chhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIIDK-NVVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~~-~~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      |-|++.++.|..- +-.|.+-|-.++.+    .+.+.+|..+|++|.  ....|+..+.|-..-+|...|++++|+.+++
T Consensus       154 d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~qdAfyifeE~s--~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~  231 (299)
T KOG3081|consen  154 DLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQDAFYIFEELS--EKTPPTPLLLNGQAVCHLQLGRYEEAESLLE  231 (299)
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhhhHHHHHHHHh--cccCCChHHHccHHHHHHHhcCHHHHHHHHH
Confidence            4466666666653 45566655555543    557999999999995  3488999999999999999999999999999


Q ss_pred             Hhhhh
Q 047113           77 IMVHD   81 (145)
Q Consensus        77 ~m~~~   81 (145)
                      ....+
T Consensus       232 eaL~k  236 (299)
T KOG3081|consen  232 EALDK  236 (299)
T ss_pred             HHHhc
Confidence            99843

>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=95.80  E-value=0.056  Score=41.27  Aligned_cols=86  Identities=9%  Similarity=0.048  Sum_probs=61.7

Q ss_pred             HHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHH
Q 047113           53 VTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGAC  115 (145)
Q Consensus        53 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~  115 (145)
                      .-...+++.+...+.++.|..+|+++. ...  |++  ...++..|...                 +.+......-.+-+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~-~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLR-ERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHH-hcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            344566777888999999999999998 332  553  33455555433                 33555555556668


Q ss_pred             HhccChhHHHHHHccCCCCCCCCCCCcc
Q 047113          116 RIHHNVKIGELVAKDPFHLDPKNDAYYT  143 (145)
Q Consensus       116 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~  143 (145)
                      .+.|+.+.|+.+.+++.+..|++-.+|.
T Consensus       245 l~k~~~~lAL~iAk~av~lsP~~f~~W~  272 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELSPSEFETWY  272 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhCchhHHHHH
Confidence            8999999999999999999887765543

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

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.77  E-value=0.099  Score=43.01  Aligned_cols=67  Identities=21%  Similarity=0.187  Sum_probs=48.0

Q ss_pred             hHHHHhccCCCCchhh--HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            3 DAERIFGGIIDKNVVI--WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         3 ~A~~~f~~m~~~~~~~--~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +|..+++.++.+++.+  |.-+-+-|+..|+++.|.++|-+-    +      -|+-.|+.|+++|.|+.|..+-.+..
T Consensus       750 kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~----~------~~~dai~my~k~~kw~da~kla~e~~  818 (1636)
T KOG3616|consen  750 KAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEA----D------LFKDAIDMYGKAGKWEDAFKLAEECH  818 (1636)
T ss_pred             hhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhc----c------hhHHHHHHHhccccHHHHHHHHHHhc
Confidence            5677777777655543  777778888888888888888652    2      24556777888888888777766554

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=95.70  E-value=0.048  Score=42.94  Aligned_cols=98  Identities=16%  Similarity=0.116  Sum_probs=69.3

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      +|..+.+.|-..|--.|.+++|..+|+....   ++| |...||-+--..+-...-++|...+.+.+   .++|+     
T Consensus       428 ~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~---v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rAL---qLqP~-----  496 (579)
T KOG1125|consen  428 IDPDVQSGLGVLYNLSGEFDRAVDCFEAALQ---VKPNDYLLWNRLGATLANGNRSEEAISAYNRAL---QLQPG-----  496 (579)
T ss_pred             CChhHHhhhHHHHhcchHHHHHHHHHHHHHh---cCCchHHHHHHhhHHhcCCcccHHHHHHHHHHH---hcCCC-----
Confidence            4667788888888888888888888888754   567 56688888888888888888888888877   35554     


Q ss_pred             HHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           93 ITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        93 ~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                           |      +.++-.|-=.|...|.+++|...|-....
T Consensus       497 -----y------VR~RyNlgIS~mNlG~ykEA~~hlL~AL~  526 (579)
T KOG1125|consen  497 -----Y------VRVRYNLGISCMNLGAYKEAVKHLLEALS  526 (579)
T ss_pred             -----e------eeeehhhhhhhhhhhhHHHHHHHHHHHHH
Confidence                 1      12333334456667777777766665444

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=95.68  E-value=0.11  Score=31.97  Aligned_cols=75  Identities=11%  Similarity=0.060  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHcCChH--HHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQER--EALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        19 ~~~li~a~~~~g~~~--~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      |++=-..|....+.|  +..+-++.+-. .++.|+.....+.+.+|.+-+++..|.++|+-++.+.|  +....|..+++
T Consensus        11 F~ary~~~F~~~~iD~we~rrglN~l~~-~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~--~~~~~Y~~~lq   87 (108)
T PF02284_consen   11 FDARYEKYFNRPDIDGWELRRGLNNLFG-YDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG--NKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHH-TT--HHHHHHHHHHHTT-SSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT--T-TTHHHHHHH
T ss_pred             HHHHHHHHhCCccccHHHHHHHHHHHhc-cccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--ChHHHHHHHHH
Confidence            333334444444333  66777777777 88999999999999999999999999999999985544  32337777665

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 ....

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=95.66  E-value=0.09  Score=32.01  Aligned_cols=63  Identities=13%  Similarity=0.140  Sum_probs=50.1

Q ss_pred             ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           31 QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        31 ~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      |.=++.+-++.+-. .++.|+.....+.+++|.+-+++..|.++|+-.+.+.|  .+...|..+++
T Consensus        22 D~we~rr~mN~l~~-~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~--~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFG-YDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCG--AHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--CchhhHHHHHH
Confidence            33466777777777 88999999999999999999999999999998873333  25557777765

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.

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

Probab=95.63  E-value=0.24  Score=41.13  Aligned_cols=97  Identities=14%  Similarity=0.131  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLL   98 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~   98 (145)
                      |--+-.++.+.|.+.+|+.+|..+.. ...--+...|-.+-.++...|.++.|.+.++...   ...|+           
T Consensus       417 ~~d~a~al~~~~~~~~Al~~l~~i~~-~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl---~~~p~-----------  481 (895)
T KOG2076|consen  417 YLDLADALTNIGKYKEALRLLSPITN-REGYQNAFVWYKLARCYMELGEYEEAIEFYEKVL---ILAPD-----------  481 (895)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHhc-CccccchhhhHHHHHHHHHHhhHHHHHHHHHHHH---hcCCC-----------
Confidence            44555666666666666666666554 3222244455556666666666666666666665   12222           


Q ss_pred             hcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           99 ATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        99 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                           +...-.+|-..+-+.|+.|+|.++...+...+
T Consensus       482 -----~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D  513 (895)
T KOG2076|consen  482 -----NLDARITLASLYQQLGNHEKALETLEQIINPD  513 (895)
T ss_pred             -----chhhhhhHHHHHHhcCCHHHHHHHHhcccCCC
Confidence                 33344456677889999999999999877433

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.62  E-value=0.087  Score=38.99  Aligned_cols=60  Identities=12%  Similarity=0.166  Sum_probs=53.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .+++|--++.-|    ++++++.+...-.+ .|+=||..+++.+|+.+.+.+++..|.++.-.|.
T Consensus       103 ~~~~~irlllky----~pq~~i~~l~npIq-YGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  103 TIHTWIRLLLKY----DPQKAIYTLVNPIQ-YGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             cHHHHHHHHHcc----ChHHHHHHHhCcch-hccccchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            456777777777    89999999999989 9999999999999999999999999888887777

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

Probab=95.61  E-value=0.29  Score=38.17  Aligned_cols=102  Identities=12%  Similarity=0.014  Sum_probs=79.7

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      .|..+.+-|-+.|-+.|+-.+|..++-+--  .=++.|..+.-=+-.-|....-++.+...|++..   =++|+..-|-.
T Consensus       590 ~dp~ilskl~dlydqegdksqafq~~ydsy--ryfp~nie~iewl~ayyidtqf~ekai~y~ekaa---liqp~~~kwql  664 (840)
T KOG2003|consen  590 NDPAILSKLADLYDQEGDKSQAFQCHYDSY--RYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA---LIQPNQSKWQL  664 (840)
T ss_pred             CCHHHHHHHHHHhhcccchhhhhhhhhhcc--cccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH---hcCccHHHHHH
Confidence            477889999999999999999988865531  2244477777777777888888888988888776   47899999998


Q ss_pred             HHHHHhcC------------------CCchhhHHHHHHHHHhccC
Q 047113           94 TVDLLATG------------------ETEPYVWGALLGACRIHHN  120 (145)
Q Consensus        94 li~~~~~~------------------~p~~~~~~~li~~~~~~g~  120 (145)
                      +|-.|.+.                  +.|..+...|+..+...|-
T Consensus       665 miasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  665 MIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            88777765                  5577888888888888775

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

Probab=95.61  E-value=0.13  Score=40.19  Aligned_cols=114  Identities=16%  Similarity=0.067  Sum_probs=83.3

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITVD   96 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~   96 (145)
                      |--+-.+|.+..+.++....|+....   +-| |..+|-.--....-.++++.|..=|++.+   .+.|+ ...|--+--
T Consensus       363 yI~~a~~y~d~~~~~~~~~~F~~A~~---ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai---~L~pe~~~~~iQl~~  436 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEKMWKDFNKAED---LDPENPDVYYHRGQMRFLLQQYEEAIADFQKAI---SLDPENAYAYIQLCC  436 (606)
T ss_pred             HHHHHHHHhhhhccHHHHHHHHHHHh---cCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHh---hcChhhhHHHHHHHH
Confidence            77777889999999999999988754   444 56666666666667788888888888877   34442 333332222


Q ss_pred             HHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           97 LLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        97 ~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      +..|.                -| -..+||..-..+..++++++|.+-+++..+++|+.
T Consensus       437 a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~  495 (606)
T KOG0547|consen  437 ALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPRE  495 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhcccc
Confidence            22222                44 45799999999999999999999999999988873

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

Probab=95.50  E-value=0.4  Score=35.73  Aligned_cols=132  Identities=14%  Similarity=0.137  Sum_probs=64.2

Q ss_pred             chHHHHhccCCC-C--chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH----HHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID-K--NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV----TFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~-~--~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~----~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      |.|+.+|..+.. +  -...-.-|+..|-+..+|++|+++=..... .+-++..+    -|.-+-.......++++|..+
T Consensus       124 DRAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k-~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~  202 (389)
T COG2956         124 DRAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVK-LGGQTYRVEIAQFYCELAQQALASSDVDRAREL  202 (389)
T ss_pred             hHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHH-cCCccchhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            455555554433 2  223444555556666666666665555544 33222111    223333333344555555555


Q ss_pred             HHHhhhhcC------------cCccHHHHHHHHHHHhcC---CCch--hhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           75 FDIMVHDFQ------------LDLNLEHYGITVDLLATG---ETEP--YVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        75 ~~~m~~~~~------------~~~~~~~~~~li~~~~~~---~p~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      +++.. ..+            +...-..|-.-|.++.+.   .|+.  .+-..|..+|...|+.++.+....++.+..
T Consensus       203 l~kAl-qa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~  279 (389)
T COG2956         203 LKKAL-QADKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN  279 (389)
T ss_pred             HHHHH-hhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc
Confidence            55544 111            001111122222222222   4443  467778888888888888888877766543

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.49  E-value=0.36  Score=34.70  Aligned_cols=119  Identities=10%  Similarity=0.145  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH---HHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG---ITV   95 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~---~li   95 (145)
                      |--++-|....|+.+.|..+++++..+..-.+-+.-+-.++  +--.|+++.|.++++.+. ... +.|.++|-   +++
T Consensus        55 ~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~--lEa~~~~~~A~e~y~~lL-~dd-pt~~v~~KRKlAil  130 (289)
T KOG3060|consen   55 YEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAML--LEATGNYKEAIEYYESLL-EDD-PTDTVIRKRKLAIL  130 (289)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHH--HHHhhchhhHHHHHHHHh-ccC-cchhHHHHHHHHHH
Confidence            44455556677899999999999875232222333333333  456789999999999999 333 33566654   556


Q ss_pred             HHHhcC--------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           96 DLLATG--------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        96 ~~~~~~--------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      .+-++.              .-|...|.-+-..|...|++++|--.++++.-+.|.++-+
T Consensus       131 ka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~  190 (289)
T KOG3060|consen  131 KAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLY  190 (289)
T ss_pred             HHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHH
Confidence            666665              6688999999999999999999999999988888866543

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=95.48  E-value=0.035  Score=27.10  Aligned_cols=25  Identities=12%  Similarity=0.084  Sum_probs=18.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHh
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLV   42 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m   42 (145)
                      +|+.|-..|.+.|++++|.++|++.
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4677778888888888888888773

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=95.39  E-value=0.59  Score=35.49  Aligned_cols=36  Identities=19%  Similarity=0.239  Sum_probs=30.1

Q ss_pred             CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          102 ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       102 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ..|...+.+++.++.-.|++++|.+..++|.+..|+
T Consensus       302 ~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~~  337 (374)
T PF13281_consen  302 MQDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKPP  337 (374)
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCCc
Confidence            446667888999999999999999999998887654

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=95.39  E-value=0.17  Score=42.53  Aligned_cols=119  Identities=8%  Similarity=-0.026  Sum_probs=80.6

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH-HHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV-TFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      .+...|..|+.++-..+++++|.++.+.-..   ..|+.. .|-.+-..+-+.++.+.+..+  .+.   +..+...-| 
T Consensus        29 ~n~~a~~~Li~~~~~~~~~deai~i~~~~l~---~~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l---~~~~~~~~~-   99 (906)
T PRK14720         29 SKFKELDDLIDAYKSENLTDEAKDICEEHLK---EHKKSISALYISGILSLSRRPLNDSNLL--NLI---DSFSQNLKW-   99 (906)
T ss_pred             chHHHHHHHHHHHHhcCCHHHHHHHHHHHHH---hCCcceehHHHHHHHHHhhcchhhhhhh--hhh---hhcccccch-
Confidence            4677899999999999999999999996543   455543 222222256777777776666  333   222222223 


Q ss_pred             HHHHHHhcC----CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           93 ITVDLLATG----ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        93 ~li~~~~~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      .++.-++++    ..+....-++..+|-+.|+.+++..+++++.+.+|+++..
T Consensus       100 ~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~a  152 (906)
T PRK14720        100 AIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEI  152 (906)
T ss_pred             hHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHH
Confidence            222223323    3344578888999999999999999999999998877643

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=95.34  E-value=0.17  Score=40.06  Aligned_cols=70  Identities=11%  Similarity=0.083  Sum_probs=57.8

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEH   90 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   90 (145)
                      +...|.++-......|++++|...|++...   +.|+...|..+-+.+...|+.++|.+.+++..   .+.|...|
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~---L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~---~L~P~~pt  488 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAID---LEMSWLNYVLLGKVYELKGDNRLAADAYSTAF---NLRPGENT  488 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHH---cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---hcCCCCch
Confidence            456788886667778999999999999877   44888999999999999999999999999887   34454334

>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=95.34  E-value=0.098  Score=29.91  Aligned_cols=68  Identities=4%  Similarity=-0.053  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCc-hhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           52 NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETE-PYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        52 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      ..+++.+-..+...|++++|...|++........++             ..|+ ..+++.+-..|...|++++|++.+++
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~-------------~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~   71 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGD-------------DHPDTANTLNNLGECYYRLGDYEEALEYYQK   71 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT-------------HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC-------------CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            347889999999999999999999998822111111             0122 45678889999999999999999886


Q ss_pred             CC
Q 047113          131 PF  132 (145)
Q Consensus       131 ~~  132 (145)
                      ..
T Consensus        72 al   73 (78)
T PF13424_consen   72 AL   73 (78)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

...

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

Probab=95.32  E-value=0.52  Score=37.01  Aligned_cols=122  Identities=12%  Similarity=0.170  Sum_probs=60.7

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC--cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP--NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      .|..+|+...   .+++.-|---+..=.++..+..|..+|++...   +-|  |...|- -+..--..|++..|.++|++
T Consensus        91 RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt---~lPRVdqlWyK-Y~ymEE~LgNi~gaRqifer  166 (677)
T KOG1915|consen   91 RARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVT---ILPRVDQLWYK-YIYMEEMLGNIAGARQIFER  166 (677)
T ss_pred             HHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHH---hcchHHHHHHH-HHHHHHHhcccHHHHHHHHH
Confidence            4666666443   24455555555555566666666666665433   222  222222 22222334555555665555


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      -.   ..+|+...|.+.|+.=.+.                .|++.+|--..+==.++|++..|+.+++..
T Consensus       167 W~---~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~VyerA  233 (677)
T KOG1915|consen  167 WM---EWEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYERA  233 (677)
T ss_pred             HH---cCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            44   3455555555555432222                455555544444444555555555555543

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.26  E-value=0.14  Score=37.51  Aligned_cols=74  Identities=14%  Similarity=0.167  Sum_probs=63.7

Q ss_pred             CCCCcHHHHHHHHHHhhc-----cchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC--------------------
Q 047113           47 DGKPNNVTFLSILFACSY-----SGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG--------------------  101 (145)
Q Consensus        47 ~~~p~~~~~~~ll~~~~~-----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~--------------------  101 (145)
                      +-+.|-.+|-..+..+.+     .+.++.--..++.|. ++|++-|..+|+.||+.+-+.                    
T Consensus        62 ~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~-eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~  140 (406)
T KOG3941|consen   62 PEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMK-EYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQN  140 (406)
T ss_pred             cccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHH-HhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhh
Confidence            345688889888888755     478888889999999 999999999999999999888                    


Q ss_pred             --------------CCchhhHHHHHHHHHhccCh
Q 047113          102 --------------ETEPYVWGALLGACRIHHNV  121 (145)
Q Consensus       102 --------------~p~~~~~~~li~~~~~~g~~  121 (145)
                                    -||-.+--.|++++++.|..
T Consensus       141 C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  141 CAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             HHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence                          78888889999999997754

>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=95.24  E-value=0.13  Score=32.88  Aligned_cols=54  Identities=9%  Similarity=-0.066  Sum_probs=48.1

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL   67 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~   67 (145)
                      |+...-.+++.+|+.+|++..|+++.+...+..+++.+..+|..|+.-+-....
T Consensus        50 Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   50 PTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             CCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcC
Confidence            788999999999999999999999999987669988899999999988765554

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

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.23  E-value=0.43  Score=30.23  Aligned_cols=57  Identities=12%  Similarity=0.191  Sum_probs=47.8

Q ss_pred             HHHHHHcCChHHHHHHHHHhHhhcCCCCc--HHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113           23 IASHAIHGQEREALEAFYLVIHCSDGKPN--NVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus        23 i~a~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      -.++-..|+.++|..+|++-.. .|+...  ...+-.+-+++...|+.++|..+++....
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~-~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALA-AGLSGADRRRALIQLASTLRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHH-cCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3566778999999999999988 887765  44667788888999999999999998883

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

Probab=95.20  E-value=0.69  Score=35.14  Aligned_cols=127  Identities=9%  Similarity=0.028  Sum_probs=77.2

Q ss_pred             cCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH-------HHHHHHHHHhhcc-----------------
Q 047113           10 GIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN-------VTFLSILFACSYS-----------------   65 (145)
Q Consensus        10 ~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~-------~~~~~ll~~~~~~-----------------   65 (145)
                      +|.++++..-.....+|.+.|++.+...+...|.+ .|+--|.       .+|+.+++-+...                 
T Consensus       181 ~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~k-a~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~l  259 (400)
T COG3071         181 EMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRK-AGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKL  259 (400)
T ss_pred             HhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHH-ccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHh
Confidence            44556777888888888888888888888888877 6654443       2455555555443                 


Q ss_pred             -----------------chHHHHHHHHHHhhhhcCcCccHHHHHH---------HHHHHhcC----CCchhhHHHHHHHH
Q 047113           66 -----------------GLIEEGIKVFDIMVHDFQLDLNLEHYGI---------TVDLLATG----ETEPYVWGALLGAC  115 (145)
Q Consensus        66 -----------------~~~~~a~~~~~~m~~~~~~~~~~~~~~~---------li~~~~~~----~p~~~~~~~li~~~  115 (145)
                                       |+.+.|.++..+-. +.+..|+...+-.         +++..-+.    +.+.-.+.+|-.-|
T Consensus       260 r~~p~l~~~~a~~li~l~~~~~A~~~i~~~L-k~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~  338 (400)
T COG3071         260 RNDPELVVAYAERLIRLGDHDEAQEIIEDAL-KRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLA  338 (400)
T ss_pred             hcChhHHHHHHHHHHHcCChHHHHHHHHHHH-HhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHH
Confidence                             34445555555444 4444444111100         00000000    33446778888889


Q ss_pred             HhccChhHHHHHHccCCCCCCCC
Q 047113          116 RIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus       116 ~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      .+++.+.+|...|+...+..|+.
T Consensus       339 ~k~~~w~kA~~~leaAl~~~~s~  361 (400)
T COG3071         339 LKNKLWGKASEALEAALKLRPSA  361 (400)
T ss_pred             HHhhHHHHHHHHHHHHHhcCCCh
Confidence            99999999999998766666643

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

Probab=95.14  E-value=0.47  Score=38.45  Aligned_cols=114  Identities=12%  Similarity=0.121  Sum_probs=88.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcC-----cCccHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ-----LDLNLE   89 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~-----~~~~~~   89 (145)
                      ...+|.-.|.-...+|.++-+.++|++-.+   +.|  ..-+--|...++.+++++|.+-+.....+..     ...+..
T Consensus       137 H~rIW~lyl~Fv~~~~lPets~rvyrRYLk---~~P--~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~q  211 (835)
T KOG2047|consen  137 HDRIWDLYLKFVESHGLPETSIRVYRRYLK---VAP--EAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQ  211 (835)
T ss_pred             hccchHHHHHHHHhCCChHHHHHHHHHHHh---cCH--HHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhh
Confidence            345688888888889999999999998754   344  4466777888999999999888887763221     245777


Q ss_pred             HHHHHHHHHhcC-------------------CC--chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           90 HYGITVDLLATG-------------------ET--EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        90 ~~~~li~~~~~~-------------------~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .|.-+-+..++.                   -+  -..-|++|-+-|.+.|.+++|..++++...
T Consensus       212 lw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~  276 (835)
T KOG2047|consen  212 LWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQ  276 (835)
T ss_pred             HHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            888887777777                   33  346899999999999999999999998543

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

Probab=95.04  E-value=0.72  Score=39.49  Aligned_cols=106  Identities=12%  Similarity=0.158  Sum_probs=83.1

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|+.+-.|--+.|+..+|.+-|-..       -|+..|.-+++.+.+.|.|+.-...+.... +..-+|.+.  +.||
T Consensus      1104 p~vWsqlakAQL~~~~v~dAieSyika-------dDps~y~eVi~~a~~~~~~edLv~yL~MaR-kk~~E~~id--~eLi 1173 (1666)
T KOG0985|consen 1104 PAVWSQLAKAQLQGGLVKDAIESYIKA-------DDPSNYLEVIDVASRTGKYEDLVKYLLMAR-KKVREPYID--SELI 1173 (1666)
T ss_pred             hHHHHHHHHHHHhcCchHHHHHHHHhc-------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHH-HhhcCccch--HHHH
Confidence            457999999999999999999888542       367889999999999999999888887776 444566554  4688


Q ss_pred             HHHhcC-----------CCchhhHHHHHHHHHhccChhHHHHHHccC
Q 047113           96 DLLATG-----------ETEPYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        96 ~~~~~~-----------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      -+|++.           .|+..-.-.+-+-|...|.++.|.-++...
T Consensus      1174 ~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~v 1220 (1666)
T KOG0985|consen 1174 FAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNV 1220 (1666)
T ss_pred             HHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHh
Confidence            888887           666666667777777777777777666543

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=94.98  E-value=0.084  Score=34.25  Aligned_cols=77  Identities=13%  Similarity=0.099  Sum_probs=53.6

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH--HHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHH
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKPNN--VTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLL   98 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~   98 (145)
                      .+-..+...|++++|...|+.... ..-.|+.  ...-.+-..+...|+++.|...++... ...+.|  ..+....++|
T Consensus        53 ~lA~~~~~~g~~~~A~~~l~~~~~-~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~-~~~~~~--~~~~~~Gdi~  128 (145)
T PF09976_consen   53 QLAKAAYEQGDYDEAKAALEKALA-NAPDPELKPLARLRLARILLQQGQYDEALATLQQIP-DEAFKA--LAAELLGDIY  128 (145)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHh-hCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcc-CcchHH--HHHHHHHHHH
Confidence            344778889999999999999877 5523322  234456677888999999999998765 444443  3555666666


Q ss_pred             hcC
Q 047113           99 ATG  101 (145)
Q Consensus        99 ~~~  101 (145)
                      .+.
T Consensus       129 ~~~  131 (145)
T PF09976_consen  129 LAQ  131 (145)
T ss_pred             HHC
Confidence            654

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=94.87  E-value=0.26  Score=41.44  Aligned_cols=118  Identities=10%  Similarity=0.053  Sum_probs=83.1

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      ..+-.|..+|-+.|+.++|..+|+++.+ .. +-|+...|.+-..++.. ++++|.+++.+... .-+  +..-|+.+..
T Consensus       117 ~Al~~LA~~Ydk~g~~~ka~~~yer~L~-~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~-~~i--~~kq~~~~~e  190 (906)
T PRK14720        117 LALRTLAEAYAKLNENKKLKGVWERLVK-AD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIY-RFI--KKKQYVGIEE  190 (906)
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHh-cC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHH-HHH--hhhcchHHHH
Confidence            3455677777788999999999999988 66 33788999999999999 99999999988873 211  1222333322


Q ss_pred             H---HhcCCC---------------------chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           97 L---LATGET---------------------EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        97 ~---~~~~~p---------------------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      .   ++.+.|                     -..++--+-..|....+++++..+++.+.+.+|++..
T Consensus       191 ~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~  258 (906)
T PRK14720        191 IWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNK  258 (906)
T ss_pred             HHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchh
Confidence            2   222222                     2233444446778888999999999999998887643

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=94.68  E-value=0.69  Score=33.73  Aligned_cols=83  Identities=13%  Similarity=0.245  Sum_probs=70.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhh----hcCcCccHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVH----DFQLDLNLEH   90 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~~~   90 (145)
                      +.++..++.++..-|+++.+...+++...   ..| |...|-.+|.++.+.|....|+..++.+.+    +-|++|...+
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~---~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~  229 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIE---LDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPEL  229 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHh---cCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHH
Confidence            34567788888999999999999999876   344 899999999999999999999999998874    4689999999


Q ss_pred             HHHHHHHHhcC
Q 047113           91 YGITVDLLATG  101 (145)
Q Consensus        91 ~~~li~~~~~~  101 (145)
                      ......+..+.
T Consensus       230 ~~~y~~~~~~~  240 (280)
T COG3629         230 RALYEEILRQD  240 (280)
T ss_pred             HHHHHHHhccc
Confidence            99888885554

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=94.62  E-value=1.1  Score=34.44  Aligned_cols=132  Identities=14%  Similarity=0.136  Sum_probs=85.8

Q ss_pred             chHHHHhccCCC-Cch--hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH-HHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID-KNV--VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV-TFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~-~~~--~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|++-|+.|-. |-.  --...|.-.--+.|+.+-|.+.-...   .+.-|... .+...+...|..|+|+.+.++.+.
T Consensus       137 ~~Ar~kfeAMl~dPEtRllGLRgLyleAqr~GareaAr~yAe~A---a~~Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd~  213 (531)
T COG3898         137 EDARKKFEAMLDDPETRLLGLRGLYLEAQRLGAREAARHYAERA---AEKAPQLPWAARATLEARCAAGDWDGALKLVDA  213 (531)
T ss_pred             HHHHHHHHHHhcChHHHHHhHHHHHHHHHhcccHHHHHHHHHHH---HhhccCCchHHHHHHHHHHhcCChHHHHHHHHH
Confidence            467777777754 221  22445555556677777776666554   33455433 667888999999999999999988


Q ss_pred             hhhhcCcCccHHHH--HHHHHHHhcC-------------------CCchh-hHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           78 MVHDFQLDLNLEHY--GITVDLLATG-------------------ETEPY-VWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        78 m~~~~~~~~~~~~~--~~li~~~~~~-------------------~p~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      -....-+++++.--  ..|+.+=+..                   .||.+ .--..-+++.+.|++.++-.+++.+.+.+
T Consensus       214 ~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~e  293 (531)
T COG3898         214 QRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVPAAVVAARALFRDGNLRKGSKILETAWKAE  293 (531)
T ss_pred             HHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCccchHHHHHHHHHHhccchhhhhhHHHHHHhcC
Confidence            77555566664432  3444333322                   55554 23334578889999999999999888877


Q ss_pred             C
Q 047113          136 P  136 (145)
Q Consensus       136 ~  136 (145)
                      |
T Consensus       294 P  294 (531)
T COG3898         294 P  294 (531)
T ss_pred             C
Confidence            6

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

Probab=94.52  E-value=1.2  Score=31.71  Aligned_cols=128  Identities=11%  Similarity=-0.040  Sum_probs=80.8

Q ss_pred             hHHHHhccCCC--C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            3 DAERIFGGIID--K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         3 ~A~~~f~~m~~--~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      .|++-+++.-+  | +..+|..+-..|.+.|..+.|.+-|+....   +.| +....|.----.|..|.+++|.+-|++.
T Consensus        53 ~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAls---l~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~A  129 (250)
T COG3063          53 QAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALS---LAPNNGDVLNNYGAFLCAQGRPEEAMQQFERA  129 (250)
T ss_pred             HHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHh---cCCCccchhhhhhHHHHhCCChHHHHHHHHHH
Confidence            45556664433  3 455888899999999999999999988644   456 4445566555568888999999888888


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..+-....-..+|..+.-+-.+.                .| ...+.-.+-.-..+.|++-.|...+++...
T Consensus       130 l~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~  201 (250)
T COG3063         130 LADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQ  201 (250)
T ss_pred             HhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHh
Confidence            73322222244555554433333                23 224555566666667777777666665443

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=94.50  E-value=0.54  Score=31.34  Aligned_cols=63  Identities=17%  Similarity=0.180  Sum_probs=46.0

Q ss_pred             chHHHHhccCCC--Cc----hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccch
Q 047113            2 DDAERIFGGIID--KN----VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGL   67 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~----~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~   67 (145)
                      ++|...|++.-.  |+    ...|..+...+.+.|++++|...+.+...   ..| +...+..+...+...|+
T Consensus        52 ~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603         52 AEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE---LNPKQPSALNNIAVIYHKRGE  121 (172)
T ss_pred             HHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHcCC
Confidence            567777775531  22    35799999999999999999999999765   345 45566666667776665

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

Probab=94.46  E-value=0.32  Score=37.42  Aligned_cols=35  Identities=11%  Similarity=0.056  Sum_probs=27.6

Q ss_pred             CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113          102 ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       102 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      +.+..+|..|+..|-..|++.+|..+.+...+.-|
T Consensus       365 p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~  399 (564)
T KOG1174|consen  365 PYRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQ  399 (564)
T ss_pred             hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhh
Confidence            45788999999999999999999877766444333

>PLN02789 farnesyltranstransferase

Probab=94.40  E-value=1.2  Score=33.24  Aligned_cols=119  Identities=13%  Similarity=0.114  Sum_probs=64.0

Q ss_pred             chhhHHHHHHHHHHcCCh--HHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQE--REALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~--~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      +..+|+---..+.+.|+.  ++++.+++.+.+ .. +-|...|+..--++...|.++++.+.++++. +.+.. |...|+
T Consensus       105 nyqaW~~R~~~l~~l~~~~~~~el~~~~kal~-~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I-~~d~~-N~sAW~  180 (320)
T PLN02789        105 NYQIWHHRRWLAEKLGPDAANKELEFTRKILS-LD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLL-EEDVR-NNSAWN  180 (320)
T ss_pred             chHHhHHHHHHHHHcCchhhHHHHHHHHHHHH-hC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHH-HHCCC-chhHHH
Confidence            444566554444455542  556666666654 22 1255566766666777777777777777776 33211 233333


Q ss_pred             HHHHHH-------------------h-cC----CCchhhHHHHHHHHHhc----cChhHHHHHHccCCCCCCC
Q 047113           93 ITVDLL-------------------A-TG----ETEPYVWGALLGACRIH----HNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        93 ~li~~~-------------------~-~~----~p~~~~~~~li~~~~~~----g~~~~a~~~~~~~~~~~~~  137 (145)
                      ...-++                   . +.    +.|...|+.+-..+...    ++..+|...+.+....+|.
T Consensus       181 ~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~  253 (320)
T PLN02789        181 QRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSN  253 (320)
T ss_pred             HHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCC
Confidence            222111                   1 00    34556777777777663    3345566666665554443

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

Probab=94.39  E-value=1  Score=36.77  Aligned_cols=124  Identities=14%  Similarity=0.112  Sum_probs=89.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      .+.-|-.|-..=-+.|..-+|..+|+.-+. .+ +-|..-|-..|..-.+.|+.+.|..+..+..+  .++.+...|.--
T Consensus       718 ~ipLWllLakleEk~~~~~rAR~ildrarl-kN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQ--ecp~sg~LWaEa  793 (913)
T KOG0495|consen  718 SIPLWLLLAKLEEKDGQLVRARSILDRARL-KN-PKNALLWLESIRMELRAGNKEQAELLMAKALQ--ECPSSGLLWAEA  793 (913)
T ss_pred             CchHHHHHHHHHHHhcchhhHHHHHHHHHh-cC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCccchhHHHH
Confidence            445677777777788888899999988765 33 33788899999999999999999988887762  344445555443


Q ss_pred             -------------HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           95 -------------VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        95 -------------i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                                   ++++-+|..|.++.-++-..+-...++++|+..|.+..+.+|+....+
T Consensus       794 I~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~w  854 (913)
T KOG0495|consen  794 IWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAW  854 (913)
T ss_pred             HHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHH
Confidence                         455555566777777777777777788888888888777777655433

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

Probab=94.36  E-value=0.22  Score=41.76  Aligned_cols=131  Identities=12%  Similarity=0.101  Sum_probs=93.0

Q ss_pred             CchHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            1 MDDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         1 ~~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      +++|..+|...++   .+..+|=.+-+.|...|++..|+++|....+...-+-+....+.|-.++-+.|.+.++.+....
T Consensus       662 ~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~  741 (1018)
T KOG2002|consen  662 FSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLK  741 (1018)
T ss_pred             chHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            4689999998876   3567899999999999999999999999655366555777889999999999999998887776


Q ss_pred             hhhhcCcCccHHHHHHHHHH--HhcC---CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDL--LATG---ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~--~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .. +-...-..+-||..+-.  .+..   .|-    .++=..-...+..+.|.++|.+|....+
T Consensus       742 a~-~~~p~~~~v~FN~a~v~kkla~s~lr~~k----~t~eev~~a~~~le~a~r~F~~ls~~~d  800 (1018)
T KOG2002|consen  742 AR-HLAPSNTSVKFNLALVLKKLAESILRLEK----RTLEEVLEAVKELEEARRLFTELSKNGD  800 (1018)
T ss_pred             HH-HhCCccchHHhHHHHHHHHHHHHHHhccc----ccHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            66 33323234556644432  2222   111    2222333445677999999999887554

>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=94.18  E-value=0.15  Score=32.91  Aligned_cols=99  Identities=16%  Similarity=0.123  Sum_probs=55.5

Q ss_pred             hhhHHHHHH---HHHHcCChHHHHHHHHHhHhhcC--CCCcHH--HHHH----------------HHHHhhccchHHHHH
Q 047113           16 VVIWSGMIA---SHAIHGQEREALEAFYLVIHCSD--GKPNNV--TFLS----------------ILFACSYSGLIEEGI   72 (145)
Q Consensus        16 ~~~~~~li~---a~~~~g~~~~A~~~~~~m~~~~~--~~p~~~--~~~~----------------ll~~~~~~~~~~~a~   72 (145)
                      +..|-.++.   ...+.|+.+.+...+.++....+  +-|+..  .|..                ++..+...|+++.+.
T Consensus         3 ~~~F~~~~~~a~~~~~~~~~~~~~~~~~~al~ly~G~~l~~~~~~~W~~~~r~~l~~~~~~~~~~l~~~~~~~~~~~~a~   82 (146)
T PF03704_consen    3 VDRFEALVREARAAARAGDPEEAIELLEEALALYRGDFLPDLDDEEWVEPERERLRELYLDALERLAEALLEAGDYEEAL   82 (146)
T ss_dssp             HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCHHHHH
Confidence            344555533   23556788888877777643121  222211  2222                233333455555555


Q ss_pred             HHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           73 KVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        73 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .+.+.+.   ...                +-|-..|..+|.+|.+.|+..+|.+.++++.+
T Consensus        83 ~~~~~~l---~~d----------------P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~  124 (146)
T PF03704_consen   83 RLLQRAL---ALD----------------PYDEEAYRLLMRALAAQGRRAEALRVYERYRR  124 (146)
T ss_dssp             HHHHHHH---HHS----------------TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHH---hcC----------------CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5555544   112                34667899999999999999999999998765

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.09  E-value=0.69  Score=35.09  Aligned_cols=117  Identities=13%  Similarity=0.075  Sum_probs=72.5

Q ss_pred             HHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH-HHHH
Q 047113           20 SGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT-VDLL   98 (145)
Q Consensus        20 ~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l-i~~~   98 (145)
                      .++-+++.-..++++.+-.+..++. .=.--|..-| .+-.+.+..|++.+|+++|-.+. ...+. |-.+|-++ ..+|
T Consensus       363 QsmAs~fFL~~qFddVl~YlnSi~s-YF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is-~~~ik-n~~~Y~s~LArCy  438 (557)
T KOG3785|consen  363 QSMASYFFLSFQFDDVLTYLNSIES-YFTNDDDFNL-NLAQAKLATGNYVEAEELFIRIS-GPEIK-NKILYKSMLARCY  438 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-HhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhc-Chhhh-hhHHHHHHHHHHH
Confidence            3455555556677777777776654 3222233333 35567777888888888887776 32222 44555544 3555


Q ss_pred             hcC---------------CCchhhHHHHH-HHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           99 ATG---------------ETEPYVWGALL-GACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        99 ~~~---------------~p~~~~~~~li-~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      .++               +.+..+.-.+| +.|-+.|.+--|-..|+.+..++| +|..
T Consensus       439 i~nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP-~pEn  496 (557)
T KOG3785|consen  439 IRNKKPQLAWDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDP-TPEN  496 (557)
T ss_pred             HhcCCchHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCC-Cccc
Confidence            555               22334444444 678888999999999999998888 4443

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=93.99  E-value=0.2  Score=40.83  Aligned_cols=95  Identities=11%  Similarity=0.069  Sum_probs=59.6

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .+|=.+-.+.-+.++++.|...|.....   +.| +...||.+-.++.+.++-.+|...+.+.. +.+            
T Consensus       520 ~~wf~~G~~ALqlek~q~av~aF~rcvt---L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAl-Kcn------------  583 (777)
T KOG1128|consen  520 GTWFGLGCAALQLEKEQAAVKAFHRCVT---LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEAL-KCN------------  583 (777)
T ss_pred             hHHHhccHHHHHHhhhHHHHHHHHHHhh---cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHh-hcC------------
Confidence            3444455555555566666666655432   344 34466666666666666666666655555 333            


Q ss_pred             HHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           96 DLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        96 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                            ..++..|-..+..-.+.|.+++|.+.+.++..
T Consensus       584 ------~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  584 ------YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             ------CCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence                  23556677778888889999999999988776

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=93.95  E-value=0.53  Score=34.13  Aligned_cols=76  Identities=14%  Similarity=0.134  Sum_probs=44.7

Q ss_pred             hHHHHhccCCCCch--hhHHHHHHHHHHc-CChHHHHHHHHHhHh---hcCCCC-c-HHHHHHHHHHhhccchHHHHHHH
Q 047113            3 DAERIFGGIIDKNV--VIWSGMIASHAIH-GQEREALEAFYLVIH---CSDGKP-N-NVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         3 ~A~~~f~~m~~~~~--~~~~~li~a~~~~-g~~~~A~~~~~~m~~---~~~~~p-~-~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      +|..+|...-.++.  .++..+-..|-.. |++++|++.|.+...   ..| .+ . ...+.-+...+.+.|++++|..+
T Consensus        99 ~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~  177 (282)
T PF14938_consen   99 KAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEI  177 (282)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHH
Confidence            44444444444332  3566666666666 777888777777432   023 22 1 33556777778888899999999


Q ss_pred             HHHhh
Q 047113           75 FDIMV   79 (145)
Q Consensus        75 ~~~m~   79 (145)
                      |++..
T Consensus       178 ~e~~~  182 (282)
T PF14938_consen  178 YEEVA  182 (282)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98887

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.92  E-value=0.033  Score=26.52  Aligned_cols=32  Identities=16%  Similarity=0.029  Sum_probs=27.8

Q ss_pred             hhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       106 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      .+|..+-..|...|++++|...|++..+++|+
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            46888899999999999999999999888875

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 ....

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.77  E-value=0.056  Score=25.51  Aligned_cols=33  Identities=24%  Similarity=0.174  Sum_probs=27.2

Q ss_pred             hhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113          106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus       106 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      ..|..+-..+...|++++|++.+++..++.|++
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~~   34 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPNN   34 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcCC
Confidence            356777889999999999999999998888853

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 ....

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=93.62  E-value=0.25  Score=38.81  Aligned_cols=96  Identities=17%  Similarity=0.062  Sum_probs=70.9

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCC
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGET  103 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p  103 (145)
                      ++.+..|+++.|..+|-+-.. .. ++|-+-|+.-..+++..|+++.|..=-..   ...+.|+                
T Consensus        10 naa~s~~d~~~ai~~~t~ai~-l~-p~nhvlySnrsaa~a~~~~~~~al~da~k---~~~l~p~----------------   68 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIM-LS-PTNHVLYSNRSAAYASLGSYEKALKDATK---TRRLNPD----------------   68 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHc-cC-CCccchhcchHHHHHHHhhHHHHHHHHHH---HHhcCCc----------------
Confidence            456788999999999998765 33 34888999999999999999877663333   3345553                


Q ss_pred             ch-hhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          104 EP-YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       104 ~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                       + .-|+=.-.+....|++++|..-|.+-.+.+|++...
T Consensus        69 -w~kgy~r~Gaa~~~lg~~~eA~~ay~~GL~~d~~n~~L  106 (539)
T KOG0548|consen   69 -WAKGYSRKGAALFGLGDYEEAILAYSEGLEKDPSNKQL  106 (539)
T ss_pred             -hhhHHHHhHHHHHhcccHHHHHHHHHHHhhcCCchHHH
Confidence             3 245556677778889999999998888888776543

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=93.58  E-value=1  Score=37.72  Aligned_cols=79  Identities=13%  Similarity=0.117  Sum_probs=58.5

Q ss_pred             hHHHHHHHH--HHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           18 IWSGMIASH--AIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        18 ~~~~li~a~--~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .|...+.|+  .|.|+.++|..+++.... .+.. |..|..++-..|.+.++.+++..++++..   +..|+...-..+.
T Consensus        43 ~~a~vLkaLsl~r~gk~~ea~~~Le~~~~-~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~---~~~P~eell~~lF  117 (932)
T KOG2053|consen   43 LYAKVLKALSLFRLGKGDEALKLLEALYG-LKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERAN---QKYPSEELLYHLF  117 (932)
T ss_pred             HHHHHHHHHHHHHhcCchhHHHHHhhhcc-CCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHH---hhCCcHHHHHHHH
Confidence            355555554  478899999988877644 3322 77888889999999999999999999887   4466677777777


Q ss_pred             HHHhcC
Q 047113           96 DLLATG  101 (145)
Q Consensus        96 ~~~~~~  101 (145)
                      .+|+|.
T Consensus       118 mayvR~  123 (932)
T KOG2053|consen  118 MAYVRE  123 (932)
T ss_pred             HHHHHH
Confidence            777766

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

Probab=93.58  E-value=1.5  Score=35.66  Aligned_cols=115  Identities=13%  Similarity=0.188  Sum_probs=71.1

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch----------------------HHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL----------------------IEEGIKVF   75 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~----------------------~~~a~~~~   75 (145)
                      -|++|-+-|.+.|++++|..+|.+-.. .  .....-|+.+.++|++...                      ++....-|
T Consensus       250 Lw~SLAdYYIr~g~~ekarDvyeeai~-~--v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~  326 (835)
T KOG2047|consen  250 LWCSLADYYIRSGLFEKARDVYEEAIQ-T--VMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARF  326 (835)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHH-h--heehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHH
Confidence            599999999999999999999998433 1  2345556666666655321                      12222222


Q ss_pred             HHhhhhcCc---------Cc-cHHHHHHHHHHHhcC---------------CC------chhhHHHHHHHHHhccChhHH
Q 047113           76 DIMVHDFQL---------DL-NLEHYGITVDLLATG---------------ET------EPYVWGALLGACRIHHNVKIG  124 (145)
Q Consensus        76 ~~m~~~~~~---------~~-~~~~~~~li~~~~~~---------------~p------~~~~~~~li~~~~~~g~~~~a  124 (145)
                      +.+..+..+         .| ++.+|..-++.|-..               .|      -...|..+-+-|-++|+++.|
T Consensus       327 e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV~l~e~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~a  406 (835)
T KOG2047|consen  327 ESLMNRRPLLLNSVLLRQNPHNVEEWHKRVKLYEGNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDA  406 (835)
T ss_pred             HHHHhccchHHHHHHHhcCCccHHHHHhhhhhhcCChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHH
Confidence            322211111         12 344454444433332               11      124688888999999999999


Q ss_pred             HHHHccCCCCC
Q 047113          125 ELVAKDPFHLD  135 (145)
Q Consensus       125 ~~~~~~~~~~~  135 (145)
                      +.+|++..+++
T Consensus       407 Rvifeka~~V~  417 (835)
T KOG2047|consen  407 RVIFEKATKVP  417 (835)
T ss_pred             HHHHHHhhcCC
Confidence            99999877744

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=93.57  E-value=0.54  Score=37.32  Aligned_cols=88  Identities=14%  Similarity=0.142  Sum_probs=70.2

Q ss_pred             ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHH
Q 047113           31 QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGA  110 (145)
Q Consensus        31 ~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~  110 (145)
                      .+.+..++|.++..+.+.++|....+.|--.|=-.|.|++|...|+...   .+.|+                |...||-
T Consensus       409 ~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL---~v~Pn----------------d~~lWNR  469 (579)
T KOG1125|consen  409 HLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAAL---QVKPN----------------DYLLWNR  469 (579)
T ss_pred             HHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHH---hcCCc----------------hHHHHHH
Confidence            3556778888877657766677777777667888899999999998888   34554                7778999


Q ss_pred             HHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          111 LLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       111 li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      |-...+...+-++|...+.+..++.|.
T Consensus       470 LGAtLAN~~~s~EAIsAY~rALqLqP~  496 (579)
T KOG1125|consen  470 LGATLANGNRSEEAISAYNRALQLQPG  496 (579)
T ss_pred             hhHHhcCCcccHHHHHHHHHHHhcCCC
Confidence            999999999999999999999998884

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=93.52  E-value=0.54  Score=31.14  Aligned_cols=73  Identities=18%  Similarity=0.242  Sum_probs=51.5

Q ss_pred             chHHHHhccCC--CC----chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhh-------ccch
Q 047113            2 DDAERIFGGII--DK----NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACS-------YSGL   67 (145)
Q Consensus         2 ~~A~~~f~~m~--~~----~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~-------~~~~   67 (145)
                      ++|...|+...  .+    ...+|..+-..+...|++++|...++.... .  .| ...+++.+...+.       ..|+
T Consensus        52 ~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~-~--~~~~~~~~~~la~i~~~~~~~~~~~g~  128 (168)
T CHL00033         52 AEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE-R--NPFLPQALNNMAVICHYRGEQAIEQGD  128 (168)
T ss_pred             HHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CcCcHHHHHHHHHHHHHhhHHHHHccc
Confidence            46667666542  12    235899999999999999999999999765 2  34 4556777777777       7777


Q ss_pred             HHHHHHHHHH
Q 047113           68 IEEGIKVFDI   77 (145)
Q Consensus        68 ~~~a~~~~~~   77 (145)
                      ++.|...+++
T Consensus       129 ~~~A~~~~~~  138 (168)
T CHL00033        129 SEIAEAWFDQ  138 (168)
T ss_pred             HHHHHHHHHH
Confidence            7755555543

>PRK15331 chaperone protein SicA; Provisional

Probab=93.50  E-value=1.3  Score=29.76  Aligned_cols=54  Identities=13%  Similarity=0.135  Sum_probs=40.8

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .-+.+.|++++|..+|+.+.. .+.- |..-|..|-.+|-..++++.|...|....
T Consensus        45 y~~y~~Gk~~eA~~~F~~L~~-~d~~-n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~   98 (165)
T PRK15331         45 YEFYNQGRLDEAETFFRFLCI-YDFY-NPDYTMGLAAVCQLKKQFQKACDLYAVAF   98 (165)
T ss_pred             HHHHHCCCHHHHHHHHHHHHH-hCcC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344579999999999999876 4422 45555666666677889999999998776

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=93.41  E-value=1.5  Score=32.26  Aligned_cols=93  Identities=17%  Similarity=0.210  Sum_probs=73.8

Q ss_pred             hHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            3 DAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         3 ~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      +|...|.+-   .+.|.+=|..=-.||++.|.++.|.+--+....   +-|. ..+|..|-.++...|.++.|.+.|++.
T Consensus        99 eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~---iDp~yskay~RLG~A~~~~gk~~~A~~aykKa  175 (304)
T KOG0553|consen   99 EAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALS---IDPHYSKAYGRLGLAYLALGKYEEAIEAYKKA  175 (304)
T ss_pred             HHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHh---cChHHHHHHHHHHHHHHccCcHHHHHHHHHhh
Confidence            455555532   345777888888999999999999987776544   4564 679999999999999999999999988


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                      .   .++|+-.+|-.=++...+.
T Consensus       176 L---eldP~Ne~~K~nL~~Ae~~  195 (304)
T KOG0553|consen  176 L---ELDPDNESYKSNLKIAEQK  195 (304)
T ss_pred             h---ccCCCcHHHHHHHHHHHHH
Confidence            8   6899888888777766655

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.38  E-value=0.84  Score=33.26  Aligned_cols=119  Identities=12%  Similarity=-0.047  Sum_probs=79.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      .-++++...-..|.+.-...++++.++ ..-+-++.--..+...-.+.|+.+.|...|++.. +..-..|..+++.++..
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~-~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~ve-k~~~kL~~~q~~~~V~~  256 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIK-YYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVE-KVTQKLDGLQGKIMVLM  256 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHH-hCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHH-HHHhhhhccchhHHHHh
Confidence            345677777778888888999998887 5545577777888888999999999999999777 33323444444444322


Q ss_pred             HhcC----------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           98 LATG----------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        98 ~~~~----------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      -.+.                      ..|...-|+---...-.|+..+|....+.+++..|..
T Consensus       257 n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~~  319 (366)
T KOG2796|consen  257 NSAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPRH  319 (366)
T ss_pred             hhhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCcc
Confidence            1111                      2233434433333344688899999999888877743

>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=93.09  E-value=2.9  Score=33.34  Aligned_cols=96  Identities=16%  Similarity=0.085  Sum_probs=76.2

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      +|.-+-..|-..|++++|++..+...+   ..|+ +.-|..--..+.+.|++++|.+..+... .-  .+          
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~---htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar-~L--D~----------  259 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIE---HTPTLVELYMTKARILKHAGDLKEAAEAMDEAR-EL--DL----------  259 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHh---cCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH-hC--Ch----------
Confidence            345556777899999999999998766   3565 6688888999999999999999998887 22  21          


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                            -|.+.=+-..+.+-+.|++++|..++....+-+
T Consensus       260 ------~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~  292 (517)
T PF12569_consen  260 ------ADRYINSKCAKYLLRAGRIEEAEKTASLFTRED  292 (517)
T ss_pred             ------hhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCC
Confidence                  266666777888899999999999998876633

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 [], [].

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=93.05  E-value=0.28  Score=24.90  Aligned_cols=27  Identities=19%  Similarity=0.226  Sum_probs=22.0

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHh
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIH   44 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~   44 (145)
                      .|..+-.+|.+.|++++|.++|++..+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            567777888888888888888888765

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.95  E-value=0.15  Score=24.81  Aligned_cols=27  Identities=7%  Similarity=-0.060  Sum_probs=22.6

Q ss_pred             hHHHHHHHHHhccChhHHHHHHccCCC
Q 047113          107 VWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      +|+.|-..|.+.|++++|..++++...
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~   27 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALA   27 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            578899999999999999999998443

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.87  E-value=0.31  Score=22.95  Aligned_cols=28  Identities=18%  Similarity=0.142  Sum_probs=21.6

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIH   44 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~   44 (145)
                      .+|..+-.++...|++++|+..|++..+
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            3677888888888888888888888654

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 ....

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=92.81  E-value=1  Score=33.57  Aligned_cols=103  Identities=13%  Similarity=-0.108  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      +-+..|.-+...|+...|.++-.+.+     .||-.-|-..+.++++.++|++-..+-.. + +     ++..|-.++++
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk-----v~dkrfw~lki~aLa~~~~w~eL~~fa~s-k-K-----sPIGyepFv~~  246 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK-----VPDKRFWWLKIKALAENKDWDELEKFAKS-K-K-----SPIGYEPFVEA  246 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC-----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC-C-C-----CCCChHHHHHH
Confidence            55666778888899888888877653     37888899999999999999877665332 1 1     23556667777


Q ss_pred             HhcC---------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           98 LATG---------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        98 ~~~~---------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      |.+.         -|- ..+..-+..|.+.|++.+|.+..-+.+.
T Consensus       247 ~~~~~~~~eA~~yI~k-~~~~~rv~~y~~~~~~~~A~~~A~~~kd  290 (319)
T PF04840_consen  247 CLKYGNKKEASKYIPK-IPDEERVEMYLKCGDYKEAAQEAFKEKD  290 (319)
T ss_pred             HHHCCCHHHHHHHHHh-CChHHHHHHHHHCCCHHHHHHHHHHcCC
Confidence            6666         111 3346678888999999888777655444

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

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=92.77  E-value=0.66  Score=30.32  Aligned_cols=119  Identities=13%  Similarity=0.072  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      .|+.-..+ .+.|++++|.+.|+.+....-..| ....---++.++-+.++++.|...++++...+--.|+ .-|...+.
T Consensus        13 ly~~a~~~-l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~-vdYa~Y~~   90 (142)
T PF13512_consen   13 LYQEAQEA-LQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPN-VDYAYYMR   90 (142)
T ss_pred             HHHHHHHH-HHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCC-ccHHHHHH
Confidence            34444443 578999999999999875333333 3446677888999999999999999999832222222 23444444


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      +++.-..+..++..+...=...+....|+.-|+.+.+.-|+.
T Consensus        91 gL~~~~~~~~~~~~~~~~drD~~~~~~A~~~f~~lv~~yP~S  132 (142)
T PF13512_consen   91 GLSYYEQDEGSLQSFFRSDRDPTPARQAFRDFEQLVRRYPNS  132 (142)
T ss_pred             HHHHHHHhhhHHhhhcccccCcHHHHHHHHHHHHHHHHCcCC
Confidence            333321111111111111122344567777777776666644

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=92.74  E-value=0.35  Score=23.64  Aligned_cols=27  Identities=19%  Similarity=0.209  Sum_probs=19.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVI   43 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~   43 (145)
                      .+++.|-..|...|++++|..++++..
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            467777777888888888888777753

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.73  E-value=2.7  Score=31.32  Aligned_cols=77  Identities=12%  Similarity=0.079  Sum_probs=47.9

Q ss_pred             HHHhccCCC-CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcC
Q 047113            5 ERIFGGIID-KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ   83 (145)
Q Consensus         5 ~~~f~~m~~-~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~   83 (145)
                      +.+.++.+. .+..+-+..-....+.|++++|.+-|....+.+|+.| ...||..+-.+ +.++++.|....+++. ..|
T Consensus       132 rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqp-llAYniALaHy-~~~qyasALk~iSEIi-eRG  208 (459)
T KOG4340|consen  132 RSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQP-LLAYNLALAHY-SSRQYASALKHISEII-ERG  208 (459)
T ss_pred             HHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCc-hhHHHHHHHHH-hhhhHHHHHHHHHHHH-Hhh
Confidence            344444442 3333444444455678888888888888665467665 45677766443 5577778888777777 555


Q ss_pred             c
Q 047113           84 L   84 (145)
Q Consensus        84 ~   84 (145)
                      +
T Consensus       209 ~  209 (459)
T KOG4340|consen  209 I  209 (459)
T ss_pred             h
Confidence            4

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=92.72  E-value=1.8  Score=32.29  Aligned_cols=108  Identities=15%  Similarity=0.063  Sum_probs=74.8

Q ss_pred             hHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhc
Q 047113            3 DAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDF   82 (145)
Q Consensus         3 ~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~   82 (145)
                      .|.++-.+.+-||..=|-.-|.+++..++|++-..+-.     +  +-.+.-|-..+.+|.+.|+..+|..+..++. . 
T Consensus       195 ~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~-----s--kKsPIGyepFv~~~~~~~~~~eA~~yI~k~~-~-  265 (319)
T PF04840_consen  195 QAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAK-----S--KKSPIGYEPFVEACLKYGNKKEASKYIPKIP-D-  265 (319)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHh-----C--CCCCCChHHHHHHHHHCCCHHHHHHHHHhCC-h-
Confidence            46666666677888889999999999999998776543     2  2345889999999999999999988887754 1 


Q ss_pred             CcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           83 QLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        83 ~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                               .--+.+|.++    ..|.-.+..+.+.++.+.=..+.++..
T Consensus       266 ---------~~rv~~y~~~----~~~~~A~~~A~~~kd~~~L~~i~~~~~  302 (319)
T PF04840_consen  266 ---------EERVEMYLKC----GDYKEAAQEAFKEKDIDLLKQILKRCP  302 (319)
T ss_pred             ---------HHHHHHHHHC----CCHHHHHHHHHHcCCHHHHHHHHHHCC
Confidence                     2223333333    234445666666666655555555443

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

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=92.63  E-value=2.9  Score=30.30  Aligned_cols=97  Identities=12%  Similarity=0.019  Sum_probs=58.9

Q ss_pred             hHHHHhccCCCC--chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC-----CCCcHH-HHHHHHHHhhccchHHHHHHH
Q 047113            3 DAERIFGGIIDK--NVVIWSGMIASHAIHGQEREALEAFYLVIHCSD-----GKPNNV-TFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         3 ~A~~~f~~m~~~--~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~-----~~p~~~-~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      +|.++|+.-..+  -..++..+...+.+.|++++|.++|++... .-     .+++.. .|-..+-++-..|+...|...
T Consensus       140 ~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~-~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~  218 (282)
T PF14938_consen  140 KAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAK-KCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKA  218 (282)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH-TCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-HhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            455555544432  234688888999999999999999998765 32     233443 333344466678899999999


Q ss_pred             HHHhhhh-cCcCcc--HHHHHHHHHHHhc
Q 047113           75 FDIMVHD-FQLDLN--LEHYGITVDLLAT  100 (145)
Q Consensus        75 ~~~m~~~-~~~~~~--~~~~~~li~~~~~  100 (145)
                      +++.... .++..+  ...-..||.+|-.
T Consensus       219 ~~~~~~~~~~F~~s~E~~~~~~l~~A~~~  247 (282)
T PF14938_consen  219 LERYCSQDPSFASSREYKFLEDLLEAYEE  247 (282)
T ss_dssp             HHHHGTTSTTSTTSHHHHHHHHHHHHHHT
T ss_pred             HHHHHhhCCCCCCcHHHHHHHHHHHHHHh
Confidence            9988732 345433  3333344444443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.44  E-value=1.2  Score=32.12  Aligned_cols=79  Identities=14%  Similarity=0.119  Sum_probs=55.9

Q ss_pred             chHHHHhccCCC--Cch----hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID--KNV----VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~----~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|...|+....  |+.    ..+--+-.+|...|++++|...|..+.....-.| ....+--+...+...|+.+.|..+
T Consensus       160 ~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~  239 (263)
T PRK10803        160 DDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAV  239 (263)
T ss_pred             HHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHH
Confidence            466777776642  433    4677888999999999999999999864122222 123333445567789999999999


Q ss_pred             HHHhhh
Q 047113           75 FDIMVH   80 (145)
Q Consensus        75 ~~~m~~   80 (145)
                      ++.+..
T Consensus       240 ~~~vi~  245 (263)
T PRK10803        240 YQQVIK  245 (263)
T ss_pred             HHHHHH
Confidence            999883

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=92.43  E-value=2.1  Score=28.26  Aligned_cols=95  Identities=13%  Similarity=0.037  Sum_probs=64.8

Q ss_pred             HHcCChHHHHHHHHHhHhhcCCCCc---HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC--
Q 047113           27 AIHGQEREALEAFYLVIHCSDGKPN---NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG--  101 (145)
Q Consensus        27 ~~~g~~~~A~~~~~~m~~~~~~~p~---~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~--  101 (145)
                      .+.++++++..+++.|+-   +.|+   ..+|-..+  +...|+|++|.++|+.+. ..+-.   ..|..-+.++|-.  
T Consensus        21 L~~~d~~D~e~lLdALrv---LrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~-~~~~~---~p~~kAL~A~CL~al   91 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRV---LRPNLKELDMFDGWL--LIARGNYDEAARILRELL-SSAGA---PPYGKALLALCLNAK   91 (153)
T ss_pred             HhcCCHHHHHHHHHHHHH---hCCCccccchhHHHH--HHHcCCHHHHHHHHHhhh-ccCCC---chHHHHHHHHHHHhc
Confidence            358999999999999965   5554   45777666  789999999999999998 33311   1355455555544  


Q ss_pred             -CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113          102 -ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus       102 -~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                       .|++..   .-......|.-.++..+.+.+..
T Consensus        92 ~Dp~Wr~---~A~~~le~~~~~~a~~Lv~al~g  121 (153)
T TIGR02561        92 GDAEWHV---HADEVLARDADADAVALVRALLG  121 (153)
T ss_pred             CChHHHH---HHHHHHHhCCCHhHHHHHHHHhc
Confidence             555444   44444466666777777776654

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=92.15  E-value=2.7  Score=33.60  Aligned_cols=77  Identities=14%  Similarity=0.113  Sum_probs=63.1

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      |+.+|+.||.-+... -++++.+.+++|..  -++-....|..-|..--...+++..+.+|.+.. ..  ..++..|...
T Consensus        19 di~sw~~lire~qt~-~~~~~R~~YEq~~~--~FP~s~r~W~~yi~~El~skdfe~VEkLF~RCL-vk--vLnlDLW~lY   92 (656)
T KOG1914|consen   19 DIDSWSQLIREAQTQ-PIDKVRETYEQLVN--VFPSSPRAWKLYIERELASKDFESVEKLFSRCL-VK--VLNLDLWKLY   92 (656)
T ss_pred             cHHHHHHHHHHHccC-CHHHHHHHHHHHhc--cCCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH-HH--HhhHhHHHHH
Confidence            899999999987666 99999999999842  333467789999999999999999999999998 22  4457778777


Q ss_pred             HHH
Q 047113           95 VDL   97 (145)
Q Consensus        95 i~~   97 (145)
                      |+-
T Consensus        93 l~Y   95 (656)
T KOG1914|consen   93 LSY   95 (656)
T ss_pred             HHH
Confidence            763

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.96  E-value=0.18  Score=24.33  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=20.6

Q ss_pred             CCchhhHHHHHHHHHHcCChHHHH
Q 047113           13 DKNVVIWSGMIASHAIHGQEREAL   36 (145)
Q Consensus        13 ~~~~~~~~~li~a~~~~g~~~~A~   36 (145)
                      +.|...|+.|-..+.+.|++++|.
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            447889999999999999999886

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=91.96  E-value=2.4  Score=33.47  Aligned_cols=71  Identities=14%  Similarity=0.014  Sum_probs=51.2

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHH
Q 047113           22 MIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGI   93 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~   93 (145)
                      |-..+-+.|+.++|.+.|++|.++....-+....-.++.++-..+.+.+++.++.+-. +...+.+ .-.|+.
T Consensus       265 LAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYd-Di~lpkSAti~YTa  336 (539)
T PF04184_consen  265 LAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYD-DISLPKSATICYTA  336 (539)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhc-cccCCchHHHHHHH
Confidence            4445557899999999999986524333345577889999999999999999999876 4443322 444554

The molecular function of this protein is uncertain.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=91.87  E-value=4.6  Score=33.49  Aligned_cols=116  Identities=16%  Similarity=0.180  Sum_probs=80.7

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITV   95 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li   95 (145)
                      .|...-+.+.+.+..++|..++.+...   +.| ....|.-.-...-..|++.+|.+.|....   -+.|+ +..-+++.
T Consensus       652 lwllaa~~~~~~~~~~~a~~CL~Ea~~---~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al---~ldP~hv~s~~Ala  725 (799)
T KOG4162|consen  652 LWLLAADLFLLSGNDDEARSCLLEASK---IDPLSASVYYLRGLLLEVKGQLEEAKEAFLVAL---ALDPDHVPSMTALA  725 (799)
T ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHh---cchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHH---hcCCCCcHHHHHHH
Confidence            466777778888888888888877643   333 44455544455666777778877777665   34553 55555555


Q ss_pred             HHHhcC-------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           96 DLLATG-------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        96 ~~~~~~-------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      .++.+.                   +.+...|=.+-..+...|+.+.|-+.|.-..++++.+|
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            555544                   44557899999999999999999999998777665444

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

Probab=91.69  E-value=2.2  Score=33.11  Aligned_cols=37  Identities=14%  Similarity=0.071  Sum_probs=30.1

Q ss_pred             CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113          102 ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus       102 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      .||..-.+.|-+.+...+.+.+|...|....+++|.+
T Consensus       468 ~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~  504 (564)
T KOG1174|consen  468 FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQDPKS  504 (564)
T ss_pred             ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCccc
Confidence            7788888888888888888888888888877777754

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=91.50  E-value=0.86  Score=33.56  Aligned_cols=90  Identities=10%  Similarity=0.146  Sum_probs=64.7

Q ss_pred             chHHHHhccCCC-------CchhhHHHHHHHHHHcCC----hHHHHHHHHHhHhhcCCCCc-H-HHHHHHHHHhhccch-
Q 047113            2 DDAERIFGGIID-------KNVVIWSGMIASHAIHGQ----EREALEAFYLVIHCSDGKPN-N-VTFLSILFACSYSGL-   67 (145)
Q Consensus         2 ~~A~~~f~~m~~-------~~~~~~~~li~a~~~~g~----~~~A~~~~~~m~~~~~~~p~-~-~~~~~ll~~~~~~~~-   67 (145)
                      .+|.++++.|++       ++-..+.+|+..  +.++    .+++..+|+.+.. .|+..+ . ...+.++..+....+ 
T Consensus       120 ~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~-~~f~kgn~LQ~LS~iLaL~~~~~~~  196 (297)
T PF13170_consen  120 QRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVEELAERMEQCYQKLAD-AGFKKGNDLQFLSHILALSEGDDQE  196 (297)
T ss_pred             HHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHHHHHHHHHHHHHHHHH-hCCCCCcHHHHHHHHHHhccccchH
Confidence            478899999975       345667777665  3333    5688899999988 898884 3 355666655544433 


Q ss_pred             -HHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           68 -IEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        68 -~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                       +.++.++++.+. +.|+.+...+|..+.
T Consensus       197 ~v~r~~~l~~~l~-~~~~kik~~~yp~lG  224 (297)
T PF13170_consen  197 KVARVIELYNALK-KNGVKIKYMHYPTLG  224 (297)
T ss_pred             HHHHHHHHHHHHH-HcCCccccccccHHH
Confidence             458999999999 889988777777554

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=91.48  E-value=2  Score=27.48  Aligned_cols=51  Identities=6%  Similarity=-0.052  Sum_probs=41.7

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL   67 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~   67 (145)
                      +...-..+|..+.+.+.+......++.+.. .+ ..+...+|.++..+++...
T Consensus         6 ~~~~~~~vv~~~~~~~~~~~l~~yLe~~~~-~~-~~~~~~~~~li~ly~~~~~   56 (140)
T smart00299        6 DPIDVSEVVELFEKRNLLEELIPYLESALK-LN-SENPALQTKLIELYAKYDP   56 (140)
T ss_pred             CcCCHHHHHHHHHhCCcHHHHHHHHHHHHc-cC-ccchhHHHHHHHHHHHHCH
Confidence            344556889999999999999999999887 66 3678889999999987643

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=91.23  E-value=0.91  Score=35.29  Aligned_cols=69  Identities=9%  Similarity=0.068  Sum_probs=52.5

Q ss_pred             CC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCch-hhHHHHHHHHHhccChhHHHH
Q 047113           49 KP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEP-YVWGALLGACRIHHNVKIGEL  126 (145)
Q Consensus        49 ~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~  126 (145)
                      .| +...++.+-.++.+.|++++|...|++..   .+.|+-              ++. .+|..+-.+|...|++++|..
T Consensus        71 dP~~a~a~~NLG~AL~~lGryeEAIa~f~rAL---eL~Pd~--------------aeA~~A~yNLAcaya~LGr~dEAla  133 (453)
T PLN03098         71 DVKTAEDAVNLGLSLFSKGRVKDALAQFETAL---ELNPNP--------------DEAQAAYYNKACCHAYREEGKKAAD  133 (453)
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---hhCCCc--------------hHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            44 57789999999999999999999999987   345541              111 346777788888888888888


Q ss_pred             HHccCCCC
Q 047113          127 VAKDPFHL  134 (145)
Q Consensus       127 ~~~~~~~~  134 (145)
                      .+++..+.
T Consensus       134 ~LrrALel  141 (453)
T PLN03098        134 CLRTALRD  141 (453)
T ss_pred             HHHHHHHh
Confidence            88876653

>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=91.07  E-value=3.5  Score=27.92  Aligned_cols=62  Identities=15%  Similarity=0.076  Sum_probs=53.0

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc--HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN--NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ..|..+..-|++.|+.++|.+.|.+++. .-..|.  ...+-.+|..+...+++..+.....+..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~-~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARD-YCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhh-hcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3688999999999999999999999987 666664  4477888999999999999888888776

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.

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

Probab=91.03  E-value=7.5  Score=32.10  Aligned_cols=60  Identities=10%  Similarity=0.120  Sum_probs=26.9

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .+|=.-+..-..+..+++|..+|...+.   ..|+...|.--++.--..+++++|.+++++..
T Consensus       619 eiwlaavKle~en~e~eraR~llakar~---~sgTeRv~mKs~~~er~ld~~eeA~rllEe~l  678 (913)
T KOG0495|consen  619 EIWLAAVKLEFENDELERARDLLAKARS---ISGTERVWMKSANLERYLDNVEEALRLLEEAL  678 (913)
T ss_pred             HHHHHHHHHhhccccHHHHHHHHHHHhc---cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHH
Confidence            3444444444455555555555554432   23344444333333334444445554444443

>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=90.92  E-value=0.13  Score=24.23  Aligned_cols=32  Identities=9%  Similarity=-0.004  Sum_probs=27.0

Q ss_pred             hhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          106 YVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       106 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      .+|..+-..|...|++++|...|++..++.|+
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            35777888999999999999999988777663

...

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=90.81  E-value=3.9  Score=28.10  Aligned_cols=65  Identities=18%  Similarity=0.220  Sum_probs=45.3

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc
Q 047113           22 MIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL   86 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~   86 (145)
                      .-..+.+.|++++|...|+.+.......| -....-.+..++-+.|+++.|...++.+...+.-.|
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~   76 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSP   76 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-T
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc
Confidence            34456789999999999999876344444 234566778889999999999999999885444333

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.69  E-value=3.9  Score=29.62  Aligned_cols=103  Identities=18%  Similarity=0.132  Sum_probs=73.5

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHC---SDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      -|+.-++.+ +.|++.+|...|....+.   +-+.||..-|  |-.++-..|+++.|..+|..+.++++-.|        
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW--LGe~~y~qg~y~~Aa~~f~~~~k~~P~s~--------  212 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW--LGESLYAQGDYEDAAYIFARVVKDYPKSP--------  212 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHH--HHHHHHhcccchHHHHHHHHHHHhCCCCC--------
Confidence            488888765 788899999999998641   1234444443  56778889999999999999984433222        


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                              .-..+.-.|-....+.|+.++|..+++.+.+.-|+.+
T Consensus       213 --------KApdallKlg~~~~~l~~~d~A~atl~qv~k~YP~t~  249 (262)
T COG1729         213 --------KAPDALLKLGVSLGRLGNTDEACATLQQVIKRYPGTD  249 (262)
T ss_pred             --------CChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCCH
Confidence                    1223334456677889999999999999888766544

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=90.08  E-value=2.1  Score=32.76  Aligned_cols=26  Identities=12%  Similarity=0.065  Sum_probs=14.0

Q ss_pred             HHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           54 TFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        54 ~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .++.+.-++.+.+.+..|.+......
T Consensus       259 ~~lNlA~c~lKl~~~~~Ai~~c~kvL  284 (397)
T KOG0543|consen  259 CHLNLAACYLKLKEYKEAIESCNKVL  284 (397)
T ss_pred             HhhHHHHHHHhhhhHHHHHHHHHHHH
Confidence            44445555555555555555555544

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

Probab=90.04  E-value=2.6  Score=34.21  Aligned_cols=89  Identities=13%  Similarity=0.164  Sum_probs=55.6

Q ss_pred             HHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-------------------CC---chhhH-HH
Q 047113           54 TFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-------------------ET---EPYVW-GA  110 (145)
Q Consensus        54 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-------------------~p---~~~~~-~~  110 (145)
                      .|....-+.--.|+...|..+.+...+...-.|+...|.-....+-+.                   .+   |-..+ -+
T Consensus       145 ~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~  224 (700)
T KOG1156|consen  145 SWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFEET  224 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhh
Confidence            445555555557778888888888874333356777766555444444                   22   22221 22


Q ss_pred             HHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113          111 LLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus       111 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      --.-+.+.|++++|..++..+...+|++-.+|
T Consensus       225 ka~l~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy  256 (700)
T KOG1156|consen  225 KADLLMKLGQLEEAVKVYRRLLERNPDNLDYY  256 (700)
T ss_pred             HHHHHHHHhhHHhHHHHHHHHHhhCchhHHHH
Confidence            23456778888999999988888888765554

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=89.74  E-value=4.2  Score=26.74  Aligned_cols=83  Identities=11%  Similarity=0.095  Sum_probs=66.9

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcC--C--CCcHHHHHHHHHHhhccch-HHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSD--G--KPNNVTFLSILFACSYSGL-IEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~--~--~p~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      ..|+++.-.+.-+.+.....+++.+.....  +  ..+..+|.+++++.+...- --.+..+|..|+ +.+.+++..-|.
T Consensus        41 fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk-~~~~~~t~~dy~  119 (145)
T PF13762_consen   41 FINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLK-KNDIEFTPSDYS  119 (145)
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHH-HcCCCCCHHHHH
Confidence            478888888888899988888888754111  1  2356689999999988877 667899999999 688899999999


Q ss_pred             HHHHHHhcC
Q 047113           93 ITVDLLATG  101 (145)
Q Consensus        93 ~li~~~~~~  101 (145)
                      .+|+++.+.
T Consensus       120 ~li~~~l~g  128 (145)
T PF13762_consen  120 CLIKAALRG  128 (145)
T ss_pred             HHHHHHHcC
Confidence            999988776

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

Probab=89.65  E-value=1.9  Score=37.08  Aligned_cols=109  Identities=16%  Similarity=0.080  Sum_probs=74.4

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHH-----HhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILF-----ACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~-----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      |-.+-..|.++|...+|++.|.+...   ++..+++ +++|.     .+-..-.++.+.+.++.|. ..+++.|..+.--
T Consensus       609 ra~IAqLCEKAGL~qraLehytDl~D---IKR~vVh-th~L~pEwLv~yFg~lsve~s~eclkaml-~~NirqNlQi~VQ  683 (1666)
T KOG0985|consen  609 RAEIAQLCEKAGLLQRALEHYTDLYD---IKRVVVH-THLLNPEWLVNYFGSLSVEDSLECLKAML-SANIRQNLQIVVQ  683 (1666)
T ss_pred             HHHHHHHHHhcchHHHHHHhcccHHH---HHHHHHH-hccCCHHHHHHHHHhcCHHHHHHHHHHHH-HHHHHhhhHHHHH
Confidence            77888999999999999999988733   4433332 22221     2222334566777778887 7777777776655


Q ss_pred             HHHHHhcC-----------------------------CCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           94 TVDLLATG-----------------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        94 li~~~~~~-----------------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      +..-|...                             ..|..+.-..|.+-|+.|++.+.+++.++-.
T Consensus       684 vatky~eqlg~~~li~lFE~fks~eGL~yfLgSivn~seDpevh~KYIqAA~kt~QikEvERicresn  751 (1666)
T KOG0985|consen  684 VATKYHEQLGAQALIELFESFKSYEGLYYFLGSIVNFSEDPEVHFKYIQAACKTGQIKEVERICRESN  751 (1666)
T ss_pred             HHHHHHHHhCHHHHHHHHHhhccchhHHHHHHHHhccccCchHHHHHHHHHHhhccHHHHHHHHhccc
Confidence            55555554                             3344444567999999999999999988643

>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=89.63  E-value=4.9  Score=31.42  Aligned_cols=55  Identities=20%  Similarity=0.171  Sum_probs=37.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +...|..|-+...+.|+++-|.++|.....          |..++-.+.-.|+.+....+-+...
T Consensus       346 ~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d----------~~~L~lLy~~~g~~~~L~kl~~~a~  400 (443)
T PF04053_consen  346 DPEKWKQLGDEALRQGNIELAEECYQKAKD----------FSGLLLLYSSTGDREKLSKLAKIAE  400 (443)
T ss_dssp             THHHHHHHHHHHHHTTBHHHHHHHHHHCT-----------HHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC----------ccccHHHHHHhCCHHHHHHHHHHHH
Confidence            566888888888888888888888877543          4455555666777666666655554

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.

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=89.55  E-value=1.6  Score=36.42  Aligned_cols=95  Identities=12%  Similarity=0.030  Sum_probs=62.0

Q ss_pred             HHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-
Q 047113           23 IASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-  101 (145)
Q Consensus        23 i~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-  101 (145)
                      |.+..++..|.+|+.+++.++. .+  .-..-|.-+-+.|+..|+++.|+++|.+-- .         ++--|++|.+. 
T Consensus       739 ieaai~akew~kai~ildniqd-qk--~~s~yy~~iadhyan~~dfe~ae~lf~e~~-~---------~~dai~my~k~~  805 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQD-QK--TASGYYGEIADHYANKGDFEIAEELFTEAD-L---------FKDAIDMYGKAG  805 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhh-hc--cccccchHHHHHhccchhHHHHHHHHHhcc-h---------hHHHHHHHhccc
Confidence            3445567788888888887765 32  334567888889999999999999887654 1         33456666666 


Q ss_pred             -------------CCch--hhHHHHHHHHHhccChhHHHHHHcc
Q 047113          102 -------------ETEP--YVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus       102 -------------~p~~--~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                                   .|..  ..|-+--.-.-.+|++.+|++++-.
T Consensus       806 kw~da~kla~e~~~~e~t~~~yiakaedldehgkf~eaeqlyit  849 (1636)
T KOG3616|consen  806 KWEDAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYIT  849 (1636)
T ss_pred             cHHHHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeEE
Confidence                         3333  3444444555666776666665543

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=89.38  E-value=0.94  Score=35.32  Aligned_cols=74  Identities=15%  Similarity=0.142  Sum_probs=50.3

Q ss_pred             HHcCChHHHHHHHHHhHhhc--CCCC------------cHHHHHHHHHHhhccchHHHHHHHHHHhhh---hcCcCccHH
Q 047113           27 AIHGQEREALEAFYLVIHCS--DGKP------------NNVTFLSILFACSYSGLIEEGIKVFDIMVH---DFQLDLNLE   89 (145)
Q Consensus        27 ~~~g~~~~A~~~~~~m~~~~--~~~p------------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~~   89 (145)
                      .+.+.+.+|.+.+..=.. .  +.+|            |-.-=++..++..+.|.+++|+.++++|..   .....-+..
T Consensus        90 Y~~k~~~kal~~ls~w~~-~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d  168 (549)
T PF07079_consen   90 YKQKEYRKALQALSVWKE-QIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSD  168 (549)
T ss_pred             HHhhhHHHHHHHHHHHHh-hhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHH
Confidence            467778888877766543 2  2222            111226677888889999999998888873   123346888


Q ss_pred             HHHHHHHHHhcC
Q 047113           90 HYGITVDLLATG  101 (145)
Q Consensus        90 ~~~~li~~~~~~  101 (145)
                      +|+.++-+++++
T Consensus       169 ~yd~~vlmlsrS  180 (549)
T PF07079_consen  169 MYDRAVLMLSRS  180 (549)
T ss_pred             HHHHHHHHHhHH
Confidence            899888888887

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>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=89.07  E-value=0.6  Score=29.97  Aligned_cols=94  Identities=12%  Similarity=0.046  Sum_probs=57.8

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhc
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  100 (145)
                      .+|..+.+.+.++.....++.+.. .+-.-+....+.++..|++.+..+....+++...   ++.++     .+++.|- 
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~-~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~---~yd~~-----~~~~~c~-   81 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVK-ENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSN---NYDLD-----KALRLCE-   81 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHH-TSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSS---SS-CT-----HHHHHHH-
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHh-cccccCHHHHHHHHHHHHhcCCchHHHHHccccc---ccCHH-----HHHHHHH-
Confidence            467777778888888888888876 5555567788888888888877777776666333   22221     1222221 


Q ss_pred             CCCchhhHHHHHHHHHhccChhHHHHH
Q 047113          101 GETEPYVWGALLGACRIHHNVKIGELV  127 (145)
Q Consensus       101 ~~p~~~~~~~li~~~~~~g~~~~a~~~  127 (145)
                         ...-|...+-.|.+.|++++|..+
T Consensus        82 ---~~~l~~~a~~Ly~~~~~~~~al~i  105 (143)
T PF00637_consen   82 ---KHGLYEEAVYLYSKLGNHDEALEI  105 (143)
T ss_dssp             ---TTTSHHHHHHHHHCCTTHTTCSST
T ss_pred             ---hcchHHHHHHHHHHcccHHHHHHH
Confidence               222444455566666776666664

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.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=88.95  E-value=1.2  Score=29.15  Aligned_cols=72  Identities=13%  Similarity=0.008  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccC
Q 047113           52 NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        52 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      ...|+.-.. --+.|+++.|...|+.+..++-..|  -+=              .+--.|+.+|.+.|++++|...+++.
T Consensus        11 ~~ly~~a~~-~l~~~~Y~~A~~~le~L~~ryP~g~--ya~--------------qAqL~l~yayy~~~~y~~A~a~~~rF   73 (142)
T PF13512_consen   11 QELYQEAQE-ALQKGNYEEAIKQLEALDTRYPFGE--YAE--------------QAQLDLAYAYYKQGDYEEAIAAYDRF   73 (142)
T ss_pred             HHHHHHHHH-HHHhCCHHHHHHHHHHHHhcCCCCc--ccH--------------HHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            344444443 3568999999999999985443332  111              22234788999999999999999999


Q ss_pred             CCCCCCCCC
Q 047113          132 FHLDPKNDA  140 (145)
Q Consensus       132 ~~~~~~~~~  140 (145)
                      .++.|..+.
T Consensus        74 irLhP~hp~   82 (142)
T PF13512_consen   74 IRLHPTHPN   82 (142)
T ss_pred             HHhCCCCCC
Confidence            998886653

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=88.59  E-value=3.5  Score=32.69  Aligned_cols=55  Identities=15%  Similarity=0.062  Sum_probs=44.1

Q ss_pred             HHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           23 IASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        23 i~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      -..+.+.|++..|...|.++.. .. +-|...|+..--++.+.|.+..|..-.+...
T Consensus       365 Gne~Fk~gdy~~Av~~YteAIk-r~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~i  419 (539)
T KOG0548|consen  365 GNEAFKKGDYPEAVKHYTEAIK-RD-PEDARLYSNRAACYLKLGEYPEALKDAKKCI  419 (539)
T ss_pred             HHHHHhccCHHHHHHHHHHHHh-cC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            4667789999999999999877 54 3378899999999999999988877655554

>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=88.15  E-value=1.1  Score=19.91  Aligned_cols=22  Identities=14%  Similarity=0.092  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHcCChHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFY   40 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~   40 (145)
                      ...+-.++.+.|++++|..+++
T Consensus         4 ~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    4 RLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHh
Confidence            3456677778888888887775

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

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=87.87  E-value=6.8  Score=33.74  Aligned_cols=124  Identities=8%  Similarity=-0.141  Sum_probs=74.7

Q ss_pred             hHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHH--HHHhhccchHHHHHHHHH
Q 047113            3 DAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSI--LFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~l--l~~~~~~~~~~~a~~~~~   76 (145)
                      .|.+.|+..   ...|...+..+.+.|++...+++|..+.-.-.+   ..| -...+|-.  --.+-+.++...+..-|+
T Consensus       510 RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~q---ka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQ  586 (1238)
T KOG1127|consen  510 RAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQ---KAPAFACKENWVQRGPYYLEAHNLHGAVCEFQ  586 (1238)
T ss_pred             HHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhh---hchHHHHHhhhhhccccccCccchhhHHHHHH
Confidence            355666633   345777899999999999999999988443322   111 12222222  223445666666666665


Q ss_pred             HhhhhcCcCc-cHHHHHHHHHHHhcC----------------CCchhhHHHHHH-HHHhccChhHHHHHHccCC
Q 047113           77 IMVHDFQLDL-NLEHYGITVDLLATG----------------ETEPYVWGALLG-ACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~~~~~~~li~-~~~~~g~~~~a~~~~~~~~  132 (145)
                      ...   ...| |...|..+..+|.++                +|+..--..-+. .-|..|+++++......+.
T Consensus       587 sAL---R~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  587 SAL---RTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             HHh---cCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            555   4555 678888888888877                443321122222 2366788888887776644

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=87.75  E-value=12  Score=29.59  Aligned_cols=90  Identities=10%  Similarity=0.023  Sum_probs=69.2

Q ss_pred             HhccCCC-C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCc
Q 047113            7 IFGGIID-K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQL   84 (145)
Q Consensus         7 ~f~~m~~-~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~   84 (145)
                      +=+.+++ | |+.+|-.||.-+...|.+++..+++.+|..  -++.=...|..-|++--...++...+.+|.+.. ..  
T Consensus        31 LRerIkdNPtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~--pfp~~~~aw~ly~s~ELA~~df~svE~lf~rCL-~k--  105 (660)
T COG5107          31 LRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQLSS--PFPIMEHAWRLYMSGELARKDFRSVESLFGRCL-KK--  105 (660)
T ss_pred             HHHHhhcCchhHHHHHHHHHHHhhhhhHHHHHHHHHHhcC--CCccccHHHHHHhcchhhhhhHHHHHHHHHHHH-hh--
Confidence            3344443 3 789999999999999999999999999953  333356688888888888999999999999998 33  


Q ss_pred             CccHHHHHHHHHHHhcC
Q 047113           85 DLNLEHYGITVDLLATG  101 (145)
Q Consensus        85 ~~~~~~~~~li~~~~~~  101 (145)
                      ..++..|...++--.+.
T Consensus       106 ~l~ldLW~lYl~YIRr~  122 (660)
T COG5107         106 SLNLDLWMLYLEYIRRV  122 (660)
T ss_pred             hccHhHHHHHHHHHHhh
Confidence            34477777777644433

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=87.71  E-value=1.5  Score=32.24  Aligned_cols=40  Identities=18%  Similarity=0.203  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSIL   59 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll   59 (145)
                      ||..|....+.||+++|+.++++.++ .|+.-=..+|--.+
T Consensus       260 y~~aI~~AVk~gDi~KAL~LldEAe~-LG~~~Ar~tFik~V  299 (303)
T PRK10564        260 FNQAIKQAVKKGDVDKALKLLDEAER-LGSTSARSTFISSV  299 (303)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH-hCCchHHHHHHHHh
Confidence            77888888888888888888888888 88775555654444

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=87.53  E-value=12  Score=29.13  Aligned_cols=37  Identities=8%  Similarity=-0.105  Sum_probs=28.7

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN   52 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~   52 (145)
                      ...|.+.+...++.|+|++|+++.+.-+...-+.+|.
T Consensus       188 ~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~  224 (531)
T COG3898         188 PWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDV  224 (531)
T ss_pred             chHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhh
Confidence            3478899999999999999999999865424445543

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=87.51  E-value=1.6  Score=21.16  Aligned_cols=28  Identities=14%  Similarity=0.213  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           52 NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        52 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ..+++.+-..+...|++++|..++++..
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            4578999999999999999999999887

>smart00028 TPR Tetratricopeptide repeats

Probab=87.46  E-value=0.78  Score=19.99  Aligned_cols=31  Identities=16%  Similarity=0.018  Sum_probs=25.5

Q ss_pred             hHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          107 VWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      .|..+-..+...|++++|...+....+..|+
T Consensus         3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~   33 (34)
T smart00028        3 ALYNLGNAYLKLGDYDEALEYYEKALELDPN   33 (34)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHccCCC
Confidence            5667778889999999999999987776663

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.

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=87.45  E-value=9.5  Score=28.08  Aligned_cols=103  Identities=14%  Similarity=0.113  Sum_probs=66.0

Q ss_pred             HcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc--cchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC----
Q 047113           28 IHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY--SGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG----  101 (145)
Q Consensus        28 ~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~--~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~----  101 (145)
                      ++....+|+.+|+...-+..+..|......+++....  ......--++.+.+....+-.++..+-.+.|..+++.    
T Consensus       140 ~N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~  219 (292)
T PF13929_consen  140 RNKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWN  219 (292)
T ss_pred             hhHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHH
Confidence            3445667777777443212355577777777777655  2233344444455553445566666777777777766    


Q ss_pred             ---------------CCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113          102 ---------------ETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus       102 ---------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                                     ..|...|...|+.....|+.+-...+..+
T Consensus       220 kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  220 KLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence                           34778899999999999998888877764

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=87.41  E-value=3.7  Score=30.03  Aligned_cols=51  Identities=8%  Similarity=-0.000  Sum_probs=42.8

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHh----hcCCCCcHHHHHHHHHHhhc
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIH----CSDGKPNNVTFLSILFACSY   64 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~----~~~~~p~~~~~~~ll~~~~~   64 (145)
                      -|...|-.||.+|.++|+...|+..|+++..    +.|+.|-..+........++
T Consensus       185 ~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~~~~~~  239 (280)
T COG3629         185 YDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYEEILRQ  239 (280)
T ss_pred             cchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhcc
Confidence            3778999999999999999999999998743    47899998888877776333

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=87.33  E-value=5.3  Score=25.80  Aligned_cols=60  Identities=13%  Similarity=0.179  Sum_probs=45.6

Q ss_pred             HHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           34 EALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        34 ~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      |..+.+..+-. .++.|+....-..+.+|.+-+++..|.++|+-++.+.|  +--..|..+++
T Consensus        67 EvrkglN~l~~-yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~g--~~k~~Y~y~v~  126 (149)
T KOG4077|consen   67 EVRKGLNNLFD-YDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDKCG--AQKQVYPYYVK  126 (149)
T ss_pred             HHHHHHHhhhc-cccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHhcc--cHHHHHHHHHH
Confidence            44445555556 78999999999999999999999999999999984333  33335666654

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=87.24  E-value=17  Score=30.85  Aligned_cols=95  Identities=9%  Similarity=0.071  Sum_probs=68.5

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|..+++....   .|..|...+-..|.+.|+.++|..+|++...   .-|+..-...+..++.+.+.+..-+++==+|
T Consensus        60 ~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~---~~P~eell~~lFmayvR~~~yk~qQkaa~~L  136 (932)
T KOG2053|consen   60 DEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQ---KYPSEELLYHLFMAYVREKSYKKQQKAALQL  136 (932)
T ss_pred             hhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHh---hCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466677775543   4888999999999999999999999999854   5678888888999999999886544433333


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                      -+  .+.-+...+-++++.+...
T Consensus       137 yK--~~pk~~yyfWsV~Slilqs  157 (932)
T KOG2053|consen  137 YK--NFPKRAYYFWSVISLILQS  157 (932)
T ss_pred             HH--hCCcccchHHHHHHHHHHh
Confidence            21  2333455666666666655

>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A

Probab=86.85  E-value=0.25  Score=26.57  Aligned_cols=30  Identities=10%  Similarity=0.052  Sum_probs=24.2

Q ss_pred             HHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113          111 LLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus       111 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      +--|+.+.|++++|++..+.+.+++|++..
T Consensus         7 lAig~ykl~~Y~~A~~~~~~lL~~eP~N~Q   36 (53)
T PF14853_consen    7 LAIGHYKLGEYEKARRYCDALLEIEPDNRQ   36 (53)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHHHTTS-HH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHhhCCCcHH
Confidence            345789999999999999999999998754

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=86.83  E-value=8.5  Score=26.83  Aligned_cols=63  Identities=10%  Similarity=0.067  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcC
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ   83 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~   83 (145)
                      --.|-.+..+.|++.||...|.+-.. --+--|....-.+-.+....+++..+.+.++.+- +.+
T Consensus        92 r~rLa~al~elGr~~EA~~hy~qals-G~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~-e~~  154 (251)
T COG4700          92 RYRLANALAELGRYHEAVPHYQQALS-GIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLM-EYN  154 (251)
T ss_pred             HHHHHHHHHHhhhhhhhHHHHHHHhc-cccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHh-hcC
Confidence            34677888999999999999998764 4455578888888888888999999999998887 443

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=86.63  E-value=4.1  Score=26.93  Aligned_cols=57  Identities=18%  Similarity=0.255  Sum_probs=36.2

Q ss_pred             chHHHHhccCCC--C---chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc
Q 047113            2 DDAERIFGGIID--K---NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY   64 (145)
Q Consensus         2 ~~A~~~f~~m~~--~---~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~   64 (145)
                      +++..+++.|+.  |   ...+|...|  +.+.|+|++|.++|++..+ .+.   ...|...+.++|-
T Consensus        27 ~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~-~~~---~~p~~kAL~A~CL   88 (153)
T TIGR02561        27 YDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLS-SAG---APPYGKALLALCL   88 (153)
T ss_pred             HHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhc-cCC---CchHHHHHHHHHH
Confidence            567777776642  3   334454444  5789999999999999976 332   2244444444444

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>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=86.39  E-value=6.3  Score=26.35  Aligned_cols=51  Identities=12%  Similarity=0.079  Sum_probs=40.2

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCCc---HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKPN---NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p~---~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ..-.+.++.+++..+++-++.   ++|.   ..++-..+  +...|+|+.|.++|+.+.
T Consensus        18 ~~al~~~~~~D~e~lL~ALrv---LRP~~~e~~~~~~~l--~i~r~~w~dA~rlLr~l~   71 (160)
T PF09613_consen   18 SVALRLGDPDDAEALLDALRV---LRPEFPELDLFDGWL--HIVRGDWDDALRLLRELE   71 (160)
T ss_pred             HHHHccCChHHHHHHHHHHHH---hCCCchHHHHHHHHH--HHHhCCHHHHHHHHHHHh
Confidence            344578899999999999966   5664   34555555  788999999999999988

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=86.35  E-value=3.7  Score=30.29  Aligned_cols=70  Identities=11%  Similarity=0.160  Sum_probs=48.5

Q ss_pred             chhhHHHHHHHHHH--cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc--cc----hHHHHHHHHHHhhhhcCcC
Q 047113           15 NVVIWSGMIASHAI--HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY--SG----LIEEGIKVFDIMVHDFQLD   85 (145)
Q Consensus        15 ~~~~~~~li~a~~~--~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~--~~----~~~~a~~~~~~m~~~~~~~   85 (145)
                      ...++.++|.....  ...+++.+.+++.|.+ .|++.+..+|-+..-....  ..    .+.++..+|+.|++++.+-
T Consensus        59 ~~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~-~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fL  136 (297)
T PF13170_consen   59 HRFILAALLDISFEDPEEAFKEVLDIYEKLKE-AGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFL  136 (297)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH-hccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccc
Confidence            44556666665544  2236678889999999 9999999888664433333  33    3568999999999766653

>PRK15331 chaperone protein SicA; Provisional

Probab=86.34  E-value=3.9  Score=27.49  Aligned_cols=77  Identities=16%  Similarity=0.110  Sum_probs=60.4

Q ss_pred             CchHHHHhccCC--CC-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            1 MDDAERIFGGII--DK-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         1 ~~~A~~~f~~m~--~~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      +++|+++|.-+.  .| |..=|-.|-..+-..+.+++|+.+|...-. .+ +-|...+-.+-.++-..|+.+.|+..|..
T Consensus        53 ~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~-l~-~~dp~p~f~agqC~l~l~~~~~A~~~f~~  130 (165)
T PRK15331         53 LDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFT-LL-KNDYRPVFFTGQCQLLMRKAAKARQCFEL  130 (165)
T ss_pred             HHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cc-cCCCCccchHHHHHHHhCCHHHHHHHHHH
Confidence            367889998553  33 555577777777789999999999988655 44 23666677778889999999999999998


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus       131 a~  132 (165)
T PRK15331        131 VN  132 (165)
T ss_pred             HH
Confidence            88

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=86.28  E-value=9.9  Score=27.07  Aligned_cols=20  Identities=10%  Similarity=0.105  Sum_probs=9.7

Q ss_pred             HHhhccchHHHHHHHHHHhh
Q 047113           60 FACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .++-+.++++.|...+++..
T Consensus        77 ~ayy~~~~y~~A~~~~e~fi   96 (243)
T PRK10866         77 YAYYKNADLPLAQAAIDRFI   96 (243)
T ss_pred             HHHHhcCCHHHHHHHHHHHH
Confidence            33444455555555555444

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=85.85  E-value=5.2  Score=24.74  Aligned_cols=44  Identities=11%  Similarity=-0.010  Sum_probs=32.6

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSIL   59 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll   59 (145)
                      |++.+-.+.+.||.|.+++.-|.++|+..+.+.|-+  ...|.-++
T Consensus        43 P~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~--~~~Y~~~l   86 (108)
T PF02284_consen   43 PEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNK--KEIYPYIL   86 (108)
T ss_dssp             --HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT---TTHHHHHH
T ss_pred             CChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCh--HHHHHHHH
Confidence            778889999999999999999999999987644433  22666666

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 ....

>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=85.80  E-value=8.4  Score=25.77  Aligned_cols=41  Identities=22%  Similarity=0.362  Sum_probs=29.1

Q ss_pred             chHHHHhccCCC--Cc---hhhHHHHHHHHHHcCChHHHHHHHHHhHh
Q 047113            2 DDAERIFGGIID--KN---VVIWSGMIASHAIHGQEREALEAFYLVIH   44 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~---~~~~~~li~a~~~~g~~~~A~~~~~~m~~   44 (145)
                      ++++.+++.++.  |.   ..++...  .+.+.|+|++|.++|+++..
T Consensus        27 ~D~e~lL~ALrvLRP~~~e~~~~~~~--l~i~r~~w~dA~rlLr~l~~   72 (160)
T PF09613_consen   27 DDAEALLDALRVLRPEFPELDLFDGW--LHIVRGDWDDALRLLRELEE   72 (160)
T ss_pred             HHHHHHHHHHHHhCCCchHHHHHHHH--HHHHhCCHHHHHHHHHHHhc
Confidence            567777776642  32   3344444  46789999999999999866

>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=85.16  E-value=9.3  Score=25.74  Aligned_cols=87  Identities=5%  Similarity=-0.040  Sum_probs=42.1

Q ss_pred             HHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC------------CCchh
Q 047113           39 FYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG------------ETEPY  106 (145)
Q Consensus        39 ~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~------------~p~~~  106 (145)
                      .+.+.+ .+++|+...+..+++.+.+.|++....++    . ++++-+|...-...+-.+...            ..-..
T Consensus        17 irSl~~-~~i~~~~~L~~lli~lLi~~~~~~~L~ql----l-q~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~   90 (167)
T PF07035_consen   17 IRSLNQ-HNIPVQHELYELLIDLLIRNGQFSQLHQL----L-QYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGT   90 (167)
T ss_pred             HHHHHH-cCCCCCHHHHHHHHHHHHHcCCHHHHHHH----H-hhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhh
Confidence            334444 55666666666666666666655333222    2 233333332222222222221            11112


Q ss_pred             hHHHHHHHHHhccChhHHHHHHccC
Q 047113          107 VWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus       107 ~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      .+..++..+-..|++-+|+++.+..
T Consensus        91 ~~~~iievLL~~g~vl~ALr~ar~~  115 (167)
T PF07035_consen   91 AYEEIIEVLLSKGQVLEALRYARQY  115 (167)
T ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHc
Confidence            3455666777777777777777664

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.30  E-value=5  Score=30.66  Aligned_cols=73  Identities=18%  Similarity=0.216  Sum_probs=35.4

Q ss_pred             hHHHHhccCCCC---chhhHHHHHH-HHHHcCChHHHHHHHHHhHhhcCCCCcHHH-HHHHHHHhhccchHHHHHHHHHH
Q 047113            3 DAERIFGGIIDK---NVVIWSGMIA-SHAIHGQEREALEAFYLVIHCSDGKPNNVT-FLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         3 ~A~~~f~~m~~~---~~~~~~~li~-a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~-~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      +|+++|=.+..|   |..+|.+++. .|.+++.++.|+.+|-.+..    ..+..+ .-.+-.-|-+.+.+=-|...|+.
T Consensus       411 eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t----~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~  486 (557)
T KOG3785|consen  411 EAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKTNT----PSERFSLLQLIANDCYKANEFYYAAKAFDE  486 (557)
T ss_pred             HHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhcCC----chhHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence            355555555443   4455555443 34456666666666655432    111111 12333445555555555555555


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      +.
T Consensus       487 lE  488 (557)
T KOG3785|consen  487 LE  488 (557)
T ss_pred             HH
Confidence            54

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

Probab=84.26  E-value=4.7  Score=35.88  Aligned_cols=74  Identities=8%  Similarity=0.044  Sum_probs=49.5

Q ss_pred             HHHHhccCCC-Cc-hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            4 AERIFGGIID-KN-VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         4 A~~~f~~m~~-~~-~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      -.++|++... -| -..|-.|...|.+.+.+++|.++|+.|.++.|  -....|....+...+..+-++|..++.+..
T Consensus      1516 l~kVFeRAcqycd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL 1591 (1710)
T KOG1070|consen 1516 LKKVFERACQYCDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRAL 1591 (1710)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            3566666654 23 34688888888888888888888888876344  345567777777777666655555555433

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=84.17  E-value=3.2  Score=31.55  Aligned_cols=92  Identities=15%  Similarity=0.118  Sum_probs=58.8

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCC
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGE  102 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~  102 (145)
                      +-|.+.|.+++|+.+|..-..   +.| |.+++..--.+|-+...+..|+.-..... .        .-...+.+|+|. 
T Consensus       105 N~yFKQgKy~EAIDCYs~~ia---~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~Ai-a--------Ld~~Y~KAYSRR-  171 (536)
T KOG4648|consen  105 NTYFKQGKYEEAIDCYSTAIA---VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAI-A--------LDKLYVKAYSRR-  171 (536)
T ss_pred             hhhhhccchhHHHHHhhhhhc---cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHH-H--------hhHHHHHHHHHH-
Confidence            457789999999999987432   456 88999888889988888876666444443 1        112233444432 


Q ss_pred             CchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          103 TEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       103 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                               +.+-...|+.++|..=++...+++|.
T Consensus       172 ---------~~AR~~Lg~~~EAKkD~E~vL~LEP~  197 (536)
T KOG4648|consen  172 ---------MQARESLGNNMEAKKDCETVLALEPK  197 (536)
T ss_pred             ---------HHHHHHHhhHHHHHHhHHHHHhhCcc
Confidence                     33333455666666666666666664

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=83.77  E-value=4.1  Score=21.21  Aligned_cols=32  Identities=13%  Similarity=-0.024  Sum_probs=16.0

Q ss_pred             HHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHH
Q 047113           27 AIHGQEREALEAFYLVIHCSDGKPNNVTFLSIL   59 (145)
Q Consensus        27 ~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll   59 (145)
                      .+.|..+++..++++|++ .|+.-+...+..++
T Consensus        13 k~~GlI~~~~~~l~~l~~-~g~~is~~l~~~~L   44 (48)
T PF11848_consen   13 KRRGLISEVKPLLDRLQQ-AGFRISPKLIEEIL   44 (48)
T ss_pred             HHcCChhhHHHHHHHHHH-cCcccCHHHHHHHH
Confidence            344555555555555544 55555554444444

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=83.42  E-value=15  Score=26.59  Aligned_cols=54  Identities=17%  Similarity=0.184  Sum_probs=27.4

Q ss_pred             HcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhh
Q 047113           28 IHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus        28 ~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      +.|++++|.+-|+.+..+....| ...+.-.++-+.-+.++++.|....++....
T Consensus        46 ~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~l  100 (254)
T COG4105          46 QKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRL  100 (254)
T ss_pred             hcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            55555555555555544333333 3334444455555555555555555555533

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=83.40  E-value=0.5  Score=21.80  Aligned_cols=27  Identities=7%  Similarity=-0.137  Sum_probs=22.2

Q ss_pred             HHHHHHhccChhHHHHHHccCCCCCCC
Q 047113          111 LLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       111 li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      +-..+.+.|+.++|.+.|+++.+.-|+
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~~P~   32 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKRYPD   32 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence            456777889999999999998876664

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=83.26  E-value=4.8  Score=20.95  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=31.3

Q ss_pred             HHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           59 LFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        59 l~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      +....+.|.++++..+++.|. +.|+..+...+..++..
T Consensus         9 L~~Ak~~GlI~~~~~~l~~l~-~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen    9 LLLAKRRGLISEVKPLLDRLQ-QAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHHcCChhhHHHHHHHHH-HcCcccCHHHHHHHHHH
Confidence            334567888889999999998 99999999998887764

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>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=83.19  E-value=0.62  Score=29.91  Aligned_cols=97  Identities=19%  Similarity=0.256  Sum_probs=63.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc----HHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN----LEH   90 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~----~~~   90 (145)
                      +....+.++..|++.++.++..+.++..   ..     .-...+++.|.+.|.++.+..++.++. +..--.+    ..-
T Consensus        41 ~~~~~~~L~~ly~~~~~~~~l~~~L~~~---~~-----yd~~~~~~~c~~~~l~~~a~~Ly~~~~-~~~~al~i~~~~~~  111 (143)
T PF00637_consen   41 NPDLHTLLLELYIKYDPYEKLLEFLKTS---NN-----YDLDKALRLCEKHGLYEEAVYLYSKLG-NHDEALEILHKLKD  111 (143)
T ss_dssp             SHHHHHHHHHHHHCTTTCCHHHHTTTSS---SS-----S-CTHHHHHHHTTTSHHHHHHHHHCCT-THTTCSSTSSSTHC
T ss_pred             CHHHHHHHHHHHHhcCCchHHHHHcccc---cc-----cCHHHHHHHHHhcchHHHHHHHHHHcc-cHHHHHHHHHHHcc
Confidence            5677899999999998888888888732   11     333667888999999999999999877 3221111    111


Q ss_pred             HHHHHHHHhcCCCchhhHHHHHHHHHhccCh
Q 047113           91 YGITVDLLATGETEPYVWGALLGACRIHHNV  121 (145)
Q Consensus        91 ~~~li~~~~~~~p~~~~~~~li~~~~~~g~~  121 (145)
                      +...+ -|++..++...|..+++.|...+..
T Consensus       112 ~~~a~-e~~~~~~~~~l~~~l~~~~l~~~~~  141 (143)
T PF00637_consen  112 YEEAI-EYAKKVDDPELWEQLLKYCLDSKPF  141 (143)
T ss_dssp             SCCCT-TTGGGCSSSHHHHHHHHHHCTSTCT
T ss_pred             HHHHH-HHHHhcCcHHHHHHHHHHHHhcCcc
Confidence            11111 2333356677788888777666543

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.

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=83.09  E-value=8.1  Score=26.25  Aligned_cols=55  Identities=9%  Similarity=-0.037  Sum_probs=42.7

Q ss_pred             HHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           25 SHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        25 a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .....++.+......+...+.....|+...|..++.++...|+.++|.+...++.
T Consensus       117 ~~~~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~  171 (193)
T PF11846_consen  117 LARLPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARAR  171 (193)
T ss_pred             hhcCCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3335556665555555554436678999999999999999999999999999988

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

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

Probab=82.83  E-value=24  Score=28.71  Aligned_cols=114  Identities=12%  Similarity=0.018  Sum_probs=62.9

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHH--------HhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcC-c
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFY--------LVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLD-L   86 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~--------~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~-~   86 (145)
                      .++-=.++......|+++.|++++.        ...+ .+..|-.  ...++..+.+.++.+.|.+++........-. +
T Consensus       376 ~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~-~~~~P~~--V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t  452 (652)
T KOG2376|consen  376 KVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILE-AKHLPGT--VGAIVALYYKIKDNDSASAVLDSAIKWWRKQQT  452 (652)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhh-hccChhH--HHHHHHHHHhccCCccHHHHHHHHHHHHHHhcc
Confidence            3444556666677788888888877        5554 4444443  3445555666666666666666555211111 1


Q ss_pred             cHHHH--------------------HHHHHHHhcC-CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           87 NLEHY--------------------GITVDLLATG-ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        87 ~~~~~--------------------~~li~~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ...-.                    .+++.=..+- ++|..+-..++.+|++. ++++|..+-+++..
T Consensus       453 ~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~-d~eka~~l~k~L~p  519 (652)
T KOG2376|consen  453 GSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFNPNDTDLLVQLVTAYARL-DPEKAESLSKKLPP  519 (652)
T ss_pred             cchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCchHHHHHHHHHHHHhc-CHHHHHHHhhcCCC
Confidence            11111                    1111111110 66777777777777777 67777777666543

>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=82.76  E-value=12  Score=26.06  Aligned_cols=65  Identities=12%  Similarity=0.007  Sum_probs=25.9

Q ss_pred             HHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhc--CcCccHHHHHHHHHHHhc
Q 047113           34 EALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDF--QLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        34 ~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~--~~~~~~~~~~~li~~~~~  100 (145)
                      +|.+.|-.+.. .+..-++..--.+-.-|. ..+-+++.+++.....-.  +-.+|...+.+|.+.|-+
T Consensus       124 ~A~~~fL~~E~-~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~  190 (203)
T PF11207_consen  124 EALRRFLQLEG-TPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQK  190 (203)
T ss_pred             HHHHHHHHHcC-CCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            34444444443 332223333233333232 333444444444443211  113445555555555443

>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=82.76  E-value=11  Score=24.71  Aligned_cols=67  Identities=10%  Similarity=0.017  Sum_probs=44.6

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcC
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLD   85 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~   85 (145)
                      ..-.+..+++..+.|+-++-.+++.++.+ . -++++...--+-.+|.+-|+...+.+++.+.. +.|+.
T Consensus        86 se~vD~ALd~lv~~~kkDqLdki~~~l~k-n-~~~~p~~L~kia~Ay~klg~~r~~~ell~~AC-ekG~k  152 (161)
T PF09205_consen   86 SEYVDLALDILVKQGKKDQLDKIYNELKK-N-EEINPEFLVKIANAYKKLGNTREANELLKEAC-EKGLK  152 (161)
T ss_dssp             -HHHHHHHHHHHHTT-HHHHHHHHHHH-------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHH-HTT-H
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHhh-c-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH-HhchH
Confidence            34456777888888888888888887643 2 25677777778888888888888888888887 66654

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=82.65  E-value=4.5  Score=28.82  Aligned_cols=68  Identities=9%  Similarity=0.047  Sum_probs=47.2

Q ss_pred             HHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           54 TFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        54 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      .|.... .+.+.|+++.|...|+.+..   ..|+ ...-.+.              -.+..++-+.|++++|...+++..
T Consensus        35 ~Y~~A~-~~~~~g~y~~Ai~~f~~l~~---~yP~s~~a~~a~--------------l~la~ayy~~~~y~~A~~~~e~fi   96 (243)
T PRK10866         35 IYATAQ-QKLQDGNWKQAITQLEALDN---RYPFGPYSQQVQ--------------LDLIYAYYKNADLPLAQAAIDRFI   96 (243)
T ss_pred             HHHHHH-HHHHCCCHHHHHHHHHHHHH---hCCCChHHHHHH--------------HHHHHHHHhcCCHHHHHHHHHHHH
Confidence            444444 34668999999999999983   2332 1221222              236678889999999999999988


Q ss_pred             CCCCCCC
Q 047113          133 HLDPKND  139 (145)
Q Consensus       133 ~~~~~~~  139 (145)
                      +..|+++
T Consensus        97 ~~~P~~~  103 (243)
T PRK10866         97 RLNPTHP  103 (243)
T ss_pred             HhCcCCC
Confidence            8877665

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=82.28  E-value=5.2  Score=26.28  Aligned_cols=56  Identities=9%  Similarity=0.046  Sum_probs=46.6

Q ss_pred             CchhhHHHHHHHHHHcCC-hHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHH
Q 047113           14 KNVVIWSGMIASHAIHGQ-EREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEE   70 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~-~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~   70 (145)
                      .+-.+|++++.+.++..- ---+..+|..|++ .+.+++..-|..+|++|.+...-+.
T Consensus        77 ~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~-~~~~~t~~dy~~li~~~l~g~~~~~  133 (145)
T PF13762_consen   77 LDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKK-NDIEFTPSDYSCLIKAALRGYFHDS  133 (145)
T ss_pred             cccchHHHHHHHHccChHHHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHcCCCCcc
Confidence            356689999999988777 6678899999998 8999999999999999987744433

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

Probab=80.93  E-value=13  Score=30.18  Aligned_cols=106  Identities=8%  Similarity=-0.063  Sum_probs=68.0

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH--HHHHH
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI--TVDLL   98 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~--li~~~   98 (145)
                      +=++-+...|++++|...-..+.. .+ +-|...+-.-+-+..+.+.|+.|..+.+.=    +.   ..+++.  +=.+|
T Consensus        17 t~ln~~~~~~e~e~a~k~~~Kil~-~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~----~~---~~~~~~~~fEKAY   87 (652)
T KOG2376|consen   17 TDLNRHGKNGEYEEAVKTANKILS-IV-PDDEDAIRCKVVALIQLDKYEDALKLIKKN----GA---LLVINSFFFEKAY   87 (652)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHh-cC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhc----ch---hhhcchhhHHHHH
Confidence            335666778899999999998865 33 334556667777788999998887443322    21   112222  35566


Q ss_pred             hcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           99 ATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        99 ~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      |.-                +.|...--.--..+-+.|++++|+.+++++.+..
T Consensus        88 c~Yrlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~  140 (652)
T KOG2376|consen   88 CEYRLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNN  140 (652)
T ss_pred             HHHHcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            644                1122233333467889999999999999986643

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=80.55  E-value=11  Score=32.15  Aligned_cols=106  Identities=8%  Similarity=-0.033  Sum_probs=50.2

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc--cHHHHHHHHHHHh
Q 047113           22 MIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL--NLEHYGITVDLLA   99 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~~~~~li~~~~   99 (145)
                      |=..|-..|.|++|.++-+.-.+    ..--.||-.--.-.-..++++.|.+.|++-. ...++.  =..-|.--|.-|.
T Consensus       832 lNKlyQs~g~w~eA~eiAE~~DR----iHLr~Tyy~yA~~Lear~Di~~AleyyEK~~-~hafev~rmL~e~p~~~e~Yv  906 (1416)
T KOG3617|consen  832 LNKLYQSQGMWSEAFEIAETKDR----IHLRNTYYNYAKYLEARRDIEAALEYYEKAG-VHAFEVFRMLKEYPKQIEQYV  906 (1416)
T ss_pred             HHHHHHhcccHHHHHHHHhhccc----eehhhhHHHHHHHHHhhccHHHHHHHHHhcC-ChHHHHHHHHHhChHHHHHHH
Confidence            33444556666666666544221    2223344344444455666777777776554 222110  0111222334444


Q ss_pred             cCCCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113          100 TGETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus       100 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      +...|..-|.+--.-.-..|+.|.|+.++...+
T Consensus       907 ~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~  939 (1416)
T KOG3617|consen  907 RRKRDESLYSWWGQYLESVGEMDAALSFYSSAK  939 (1416)
T ss_pred             HhccchHHHHHHHHHHhcccchHHHHHHHHHhh
Confidence            443343444444444455666666666665543

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	145
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.94
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.87
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.83
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.56
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.54
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.22
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.11
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.08
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.03
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.03
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.0
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.98
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.98
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	98.97
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.97
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.96
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.96
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.94
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.94
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.94
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.92
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.9
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.89
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.87
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.86
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.85
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.81
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.8
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.78
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.74
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.74
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.74
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.71
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.71
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.71
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.7
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.69
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.68
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.68
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.66
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.66
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.65
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.65
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.65
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	98.65
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.63
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.63
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.62
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.62
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.62
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.61
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.6
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.6
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.6
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.59
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.57
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.57
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.56
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.54
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.53
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.52
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.52
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.51
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.51
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.51
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.5
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.49
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.48
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.47
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.44
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.44
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.43
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.42
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.42
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.41
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.4
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.37
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.35
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.31
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.31
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.28
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.27
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.26
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.26
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.26
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.23
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.2
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.19
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.18
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.18
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.17
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.17
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.16
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.16
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.15
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.15
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.1
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.1
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.1
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.09
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.08
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.08
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.05
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.05
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.04
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.03
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.02
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.01
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.0
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.99
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.99
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.98
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.93
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.89
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.87
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.86
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.85
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.84
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.83
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.81
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.79
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.78
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.76
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.76
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.75
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.75
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.74
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.73
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.73
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.69
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.69
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.68
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.68
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.68
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.67
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.67
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.66
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.66
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.65
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.65
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.64
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.63
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.63
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.62
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.61
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.61
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.61
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.61
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.6
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.59
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.57
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.56
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.49
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.45
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.45
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.43
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.38
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.36
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.35
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.33
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.33
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.33
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.3
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.29
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.25
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.23
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.22
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.22
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.21
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.21
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.21
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.18
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.13
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.1
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.07
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.05
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.02
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.97
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.96
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	96.95
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	96.89
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	96.87
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	96.81
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.8
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	96.8
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.8
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	96.71
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.54
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	96.54
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	96.51
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.51
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.5
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	96.47
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.37
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.34
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.23
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.18
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.17
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.12
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.01
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	95.75
1klx_A	138	Cysteine rich protein B; structural genomics, heli	95.65
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	95.55
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	95.39
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.34
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	95.26
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	95.22
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	95.12
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.1
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	95.07
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	95.02
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.82
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	94.59
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.25
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	93.97
1pc2_A	152	Mitochondria fission protein; unknown function; NM	93.93
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	93.85
1klx_A	138	Cysteine rich protein B; structural genomics, heli	93.74
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.29
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	93.21
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	93.08
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	92.48
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	92.45
1pc2_A	152	Mitochondria fission protein; unknown function; NM	87.34
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	87.17
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	86.01
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	84.75
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	83.86
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	82.87
3ygs_P	97	Procaspase 9; apoptosis, caspase activation, caspa	82.11
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	82.04
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	81.45
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	81.13
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	80.15
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	80.13

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.97  E-value=1.1e-30  Score=200.25  Aligned_cols=136  Identities=14%  Similarity=0.066  Sum_probs=127.2

Q ss_pred             CchHHHHhccCCC----CchhhHHHHHHHHHHcCC---------hHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch
Q 047113            1 MDDAERIFGGIID----KNVVIWSGMIASHAIHGQ---------EREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL   67 (145)
Q Consensus         1 ~~~A~~~f~~m~~----~~~~~~~~li~a~~~~g~---------~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~   67 (145)
                      +++|.++|++|+.    ||.+|||+||.+|++.+.         .++|.++|++|.. .|+.||..|||++|++|++.|+
T Consensus        42 ~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~-~G~~Pd~~tyn~lI~~~~~~g~  120 (501)
T 4g26_A           42 VLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIV-DKVVPNEATFTNGARLAVAKDD  120 (501)
T ss_dssp             HHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHH-TTCCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCC
Confidence            3689999999974    899999999999998765         6889999999999 9999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC------------------CCchhhHHHHHHHHHhccChhHHHHHHc
Q 047113           68 IEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG------------------ETEPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        68 ~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      ++.|.++|++|. +.|+.||..||++||.+|++.                  .||..+|++||++|++.|++++|.++++
T Consensus       121 ~~~A~~l~~~M~-~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~  199 (501)
T 4g26_A          121 PEMAFDMVKQMK-AFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQ  199 (501)
T ss_dssp             HHHHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-HcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence            999999999999 899999999999999999998                  9999999999999999999999999999


Q ss_pred             cCCC--CCCCC
Q 047113          130 DPFH--LDPKN  138 (145)
Q Consensus       130 ~~~~--~~~~~  138 (145)
                      +|.+  ..|+.
T Consensus       200 ~Mr~~g~~ps~  210 (501)
T 4g26_A          200 RLRDLVRQVSK  210 (501)
T ss_dssp             HHHHHTSSBCH
T ss_pred             HHHHhCCCcCH
Confidence            9988  55643

>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=99.94  E-value=1e-27  Score=183.85  Aligned_cols=136  Identities=13%  Similarity=0.139  Sum_probs=114.5

Q ss_pred             hHHHHhccCCCC-----chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc---------hH
Q 047113            3 DAERIFGGIIDK-----NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSG---------LI   68 (145)
Q Consensus         3 ~A~~~f~~m~~~-----~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~---------~~   68 (145)
                      .++.++..++++     +...++.+|++|++.|++++|.++|++|.+ .|++||..|||++|++|++.+         .+
T Consensus         8 ~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~-~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l   86 (501)
T 4g26_A            8 PSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARR-NGVQLSQYHYNVLLYVCSLAEAATESSPNPGL   86 (501)
T ss_dssp             ----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHH
T ss_pred             hHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCCHhHHHHHHHHHHhCCchhhhhhcchH
Confidence            456666777542     345799999999999999999999999999 999999999999999998755         47


Q ss_pred             HHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC------------------CCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           69 EEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG------------------ETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        69 ~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      +.|.++|++|. ..|+.||..||++||++|++.                  .||..+||++|.+|++.|++++|.++|++
T Consensus        87 ~~A~~lf~~M~-~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~  165 (501)
T 4g26_A           87 SRGFDIFKQMI-VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAH  165 (501)
T ss_dssp             HHHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHH
Confidence            89999999999 899999999999999999998                  89999999999999999999999999999


Q ss_pred             CCC--CCCCCCC
Q 047113          131 PFH--LDPKNDA  140 (145)
Q Consensus       131 ~~~--~~~~~~~  140 (145)
                      |.+  +.|+..+
T Consensus       166 M~~~G~~Pd~~t  177 (501)
T 4g26_A          166 MVESEVVPEEPE  177 (501)
T ss_dssp             HHHTTCCCCHHH
T ss_pred             HHhcCCCCCHHH
Confidence            987  5675433

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.87  E-value=1.9e-22  Score=162.42  Aligned_cols=117  Identities=11%  Similarity=0.014  Sum_probs=105.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHh--hcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIH--CSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~--~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      ..|||+||++||+.|++++|.++|++|.+  +.|+.||..|||+||+++|+.|.+++|.++|++|. ..|+.||+.|||+
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~-~~G~~PDvvTYnt  205 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVK-DAGLTPDLLSYAA  205 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-HTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHH-HcCCCCcHHHHHH
Confidence            35899999999999999999999988753  16899999999999999999999999999999999 9999999999999


Q ss_pred             HHHHHhcC-------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           94 TVDLLATG-------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        94 li~~~~~~-------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ||+++|+.                   .||..+|++++.++.+.+-++...++...+.-
T Consensus       206 LI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p  264 (1134)
T 3spa_A          206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSL  264 (1134)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCC
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCcccCC
Confidence            99999985                   89999999999999998887777777655544

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.83  E-value=3.3e-21  Score=155.29  Aligned_cols=99  Identities=10%  Similarity=0.081  Sum_probs=91.4

Q ss_pred             CchHHHHhccCC-------CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchH-HHHH
Q 047113            1 MDDAERIFGGII-------DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLI-EEGI   72 (145)
Q Consensus         1 ~~~A~~~f~~m~-------~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~-~~a~   72 (145)
                      +++|.++|++|+       .||++|||+||++||+.|++++|.++|++|.+ .|++||.+|||++|+++|+.|.. +.|.
T Consensus       143 leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~-~G~~PDvvTYntLI~glcK~G~~~e~A~  221 (1134)
T 3spa_A          143 LPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKD-AGLTPDLLSYAAALQCMGRQDQDAGTIE  221 (1134)
T ss_dssp             HHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-TTCCCCHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCcHHHHHHHHHHHHhCCCcHHHHH
Confidence            478999998764       48999999999999999999999999999999 99999999999999999999985 7899


Q ss_pred             HHHHHhhhhcCcCccHHHHHHHHHHHhcC
Q 047113           73 KVFDIMVHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        73 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                      ++|++|. ..|+.||..+|+++++.+.+.
T Consensus       222 ~Ll~EM~-~kG~~PD~vtY~~ll~~~eR~  249 (1134)
T 3spa_A          222 RCLEQMS-QEGLKLQALFTAVLLSEEDRA  249 (1134)
T ss_dssp             HHHHHHH-HHTCCSHHHHHHSCCCHHHHH
T ss_pred             HHHHHHH-HcCCCCChhhcccccChhhHH
Confidence            9999999 899999999999777766666

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.56  E-value=1.8e-14  Score=110.71  Aligned_cols=138  Identities=9%  Similarity=-0.044  Sum_probs=90.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.++|+++.   +++..+|+.++.+|.+.|++++|.++|++|.+ .. +.+..+|+.+...+.+.|++++|..+|+++
T Consensus       424 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  501 (597)
T 2xpi_A          424 DQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYA-LF-QYDPLLLNELGVVAFNKSDMQTAINHFQNA  501 (597)
T ss_dssp             HHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            45666666542   23556666677777777777777777766654 32 235666777777777777777777777776


Q ss_pred             hhhc----CcCcc--HHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           79 VHDF----QLDLN--LEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        79 ~~~~----~~~~~--~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      . ..    +..|+  ..+|..++.+|.+.                 +.+..+|..+..+|.+.|++++|...++++.+..
T Consensus       502 ~-~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~  580 (597)
T 2xpi_A          502 L-LLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAIS  580 (597)
T ss_dssp             H-HHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             H-HhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence            6 32    55665  56777777777666                 3356677777777777777777777777777777


Q ss_pred             CCCCCCc
Q 047113          136 PKNDAYY  142 (145)
Q Consensus       136 ~~~~~~~  142 (145)
                      |+++..+
T Consensus       581 p~~~~~~  587 (597)
T 2xpi_A          581 PNEIMAS  587 (597)
T ss_dssp             TTCHHHH
T ss_pred             CCChHHH
Confidence            7665444

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.54  E-value=2.8e-14  Score=109.65  Aligned_cols=135  Identities=11%  Similarity=-0.057  Sum_probs=93.5

Q ss_pred             chHHHHhccCCC--CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            2 DDAERIFGGIID--KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ++|.++|+++..  ++..+|+.++.+|.+.|++++|..+|++|.. .+ +.+..+++.++.++.+.|++++|..+++.+.
T Consensus       289 ~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  366 (597)
T 2xpi_A          289 RRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAITTKILE-ID-PYNLDVYPLHLASLHESGEKNKLYLISNDLV  366 (597)
T ss_dssp             HHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-cC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            578889998876  6888999999999999999999999999876 44 2255666777777777777777777777666


Q ss_pred             hhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           80 HDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                       .. ...+..+|+.++.+|.+.                 +.+..+|+.++.+|.+.|++++|.++|+++.+..|+++.
T Consensus       367 -~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  442 (597)
T 2xpi_A          367 -DR-HPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHL  442 (597)
T ss_dssp             -HH-CTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSH
T ss_pred             -hh-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchH
Confidence             22 133566666666666655                 234556666666666666666666666666665554443

>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=99.22  E-value=1.4e-10  Score=84.87  Aligned_cols=136  Identities=10%  Similarity=0.119  Sum_probs=110.2

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..   .+.+..+|+.+..++.+.|++++|...|+++.+ .  .| +..+|..+..++.+.|++++|...++.
T Consensus       220 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  296 (388)
T 1w3b_A          220 DRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIE-L--QPHFPDAYCNLANALKEKGSVAEAEDCYNT  296 (388)
T ss_dssp             THHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-T--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-h--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            4566666644   233678899999999999999999999999876 3  35 577889999999999999999999999


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      +. .. .+.+..+|..+...|.+.                 +.+..+|..+..+|.+.|++++|...++++.+..|+.+.
T Consensus       297 al-~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~  374 (388)
T 1w3b_A          297 AL-RL-CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFAD  374 (388)
T ss_dssp             HH-HH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHH
T ss_pred             HH-hh-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHH
Confidence            98 32 245788888898888876                 345678999999999999999999999999988887665


Q ss_pred             Cc
Q 047113          141 YY  142 (145)
Q Consensus       141 ~~  142 (145)
                      .|
T Consensus       375 a~  376 (388)
T 1w3b_A          375 AY  376 (388)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=99.11  E-value=4.1e-10  Score=83.53  Aligned_cols=135  Identities=6%  Similarity=-0.028  Sum_probs=105.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHH------------HHHhhcc
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSI------------LFACSYS   65 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~l------------l~~~~~~   65 (145)
                      ++|.+.|+.+.   +.+..+|..+...+.+.|++++|...|+++.. .  .|+ ...+..+            ...+.+.
T Consensus       194 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (450)
T 2y4t_A          194 RKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLK-L--DQDHKRCFAHYKQVKKLNKLIESAEELIRD  270 (450)
T ss_dssp             GGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCChHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            56777777663   34678899999999999999999999998865 3  343 4444444            7888899


Q ss_pred             chHHHHHHHHHHhhhhcCcCcc-----HHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhH
Q 047113           66 GLIEEGIKVFDIMVHDFQLDLN-----LEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKI  123 (145)
Q Consensus        66 ~~~~~a~~~~~~m~~~~~~~~~-----~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~  123 (145)
                      |++++|...|+.+. .  +.|+     ...|..+..+|.+.                 +.+...|..+..+|...|++++
T Consensus       271 g~~~~A~~~~~~~l-~--~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~  347 (450)
T 2y4t_A          271 GRYTDATSKYESVM-K--TEPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAEAYLIEEMYDE  347 (450)
T ss_dssp             TCHHHHHHHHHHHH-H--HCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             CCHHHHHHHHHHHH-h--cCCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHH
Confidence            99999999999988 3  3343     45777888888776                 4467899999999999999999


Q ss_pred             HHHHHccCCCCCCCCCCCc
Q 047113          124 GELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus       124 a~~~~~~~~~~~~~~~~~~  142 (145)
                      |...++++.+..|+++..+
T Consensus       348 A~~~~~~al~~~p~~~~~~  366 (450)
T 2y4t_A          348 AIQDYETAQEHNENDQQIR  366 (450)
T ss_dssp             HHHHHHHHHTTSSSCHHHH
T ss_pred             HHHHHHHHHHhCcchHHHH
Confidence            9999999999888776543

>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=99.08  E-value=4.4e-09  Score=68.40  Aligned_cols=139  Identities=10%  Similarity=-0.072  Sum_probs=113.3

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+.+..   .+...|..+...+.+.|++++|...|+.... .. +.+...+..+...+...|+++.|...++..
T Consensus        25 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~  102 (186)
T 3as5_A           25 SQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLA-DA-PDNVKVATVLGLTYVQVQKYDLAVPLLIKV  102 (186)
T ss_dssp             HHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            578888887754   3677899999999999999999999999876 32 336778899999999999999999999998


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      . .. .+.+...+..+..+|.+.                 +.+..++..+...+...|++++|...+++..+..|+++..
T Consensus       103 ~-~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  180 (186)
T 3as5_A          103 A-EA-NPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANELDEGASVE  180 (186)
T ss_dssp             H-HH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCCCGG
T ss_pred             H-hc-CcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCchhh
Confidence            8 32 234677788888777766                 4466789999999999999999999999988877766655


Q ss_pred             ccc
Q 047113          142 YTS  144 (145)
Q Consensus       142 ~~~  144 (145)
                      ..+
T Consensus       181 ~~~  183 (186)
T 3as5_A          181 LAL  183 (186)
T ss_dssp             GGG
T ss_pred             Hhh
Confidence            443

>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=99.03  E-value=5.5e-09  Score=71.79  Aligned_cols=135  Identities=9%  Similarity=-0.115  Sum_probs=88.1

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|++..   +.+...|..+...+.+.|++++|...|++... .. +.+...+..+...+...|++++|...++.+
T Consensus        54 ~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  131 (252)
T 2ho1_A           54 EQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALA-SD-SRNARVLNNYGGFLYEQKRYEEAYQRLLEA  131 (252)
T ss_dssp             GGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HC-cCcHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            45666666542   23566777777777777888888887777655 32 225667777777777777777777777777


Q ss_pred             hhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           79 VHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      . ..+..| +...+..+..+|.+.                 +.+...|..+...|...|++++|...++++.+..|+++
T Consensus       132 ~-~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~  209 (252)
T 2ho1_A          132 S-QDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNA  209 (252)
T ss_dssp             T-TCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCH
T ss_pred             H-hCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcH
Confidence            7 333344 455666666666554                 33455666777777777777777777777666555443

>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=99.03  E-value=3e-09  Score=77.76  Aligned_cols=117  Identities=15%  Similarity=0.118  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVD   96 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~   96 (145)
                      |..+...+.+.|++++|...|++...   +.| +..++..+..++.+.|+++.|...|+++. .  ..| +..+|..+..
T Consensus       206 ~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al-~--~~p~~~~~~~~l~~  279 (388)
T 1w3b_A          206 YINLGNVLKEARIFDRAVAAYLRALS---LSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAI-E--LQPHFPDAYCNLAN  279 (388)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--TCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh---hCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-h--hCCCCHHHHHHHHH
Confidence            33333333444444444444443322   234 35667777777777778888888777777 3  233 4566777777


Q ss_pred             HHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           97 LLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        97 ~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +|.+.                 +++..+|+.+...+...|++++|...++++.+..|+++..
T Consensus       280 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  341 (388)
T 1w3b_A          280 ALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAA  341 (388)
T ss_dssp             HHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHH
Confidence            77655                 5566788888888888888888888888888877765543

>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=99.00  E-value=4.5e-11  Score=89.99  Aligned_cols=119  Identities=14%  Similarity=0.156  Sum_probs=12.3

Q ss_pred             CchHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113            1 MDDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus         1 ~~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      +++|.++++++..|+  +|+.|..++.+.|++++|++.|..       .+|..+|..++.+|...|.+++|...++... 
T Consensus        19 ld~A~~fae~~~~~~--vWs~La~A~l~~g~~~eAIdsfik-------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ar-   88 (449)
T 1b89_A           19 LDRAYEFAERCNEPA--VWSQLAKAQLQKGMVKEAIDSYIK-------ADDPSSYMEVVQAANTSGNWEELVKYLQMAR-   88 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhCCChH--HHHHHHHHHHHcCCHHHHHHHHHc-------CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHH-
Confidence            478889999986654  999999999999999999999964       2678899999999999999999999887776 


Q ss_pred             hcCcCccHHHHHHHHHHHhcC-----------CCchhhHHHHHHHHHhccChhHHHHHHccC
Q 047113           81 DFQLDLNLEHYGITVDLLATG-----------ETEPYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        81 ~~~~~~~~~~~~~li~~~~~~-----------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      +  ..++..+.+.|+.+|++.           .|+..+|+.+...|...|++++|...|..+
T Consensus        89 k--~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a  148 (449)
T 1b89_A           89 K--KARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV  148 (449)
T ss_dssp             ----------------------CHHHHTTTTTCC----------------CTTTHHHHHHHT
T ss_pred             H--hCccchhHHHHHHHHHHhCCHHHHHHHHcCCcHHHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            3  256688899999999998           788889999999999999999999999876

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.98  E-value=1.6e-08  Score=72.22  Aligned_cols=129  Identities=7%  Similarity=-0.082  Sum_probs=59.3

Q ss_pred             hHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHH---HHHHHHhhccchHHHHHHHHHHhh
Q 047113            3 DAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTF---LSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         3 ~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~---~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +|.+.|+.  +.+...|..+...+.+.|++++|...|+.+.+ .  .|+....   ...+......|++++|..+|+++.
T Consensus       119 ~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~-~--~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l  193 (291)
T 3mkr_A          119 AALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQD-Q--DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMA  193 (291)
T ss_dssp             HHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-h--CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHH
Confidence            44444444  23444555555555555555555555555544 2  2332111   112222233455555555555555


Q ss_pred             hhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhH-HHHHHccCCCCCCCC
Q 047113           80 HDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKI-GELVAKDPFHLDPKN  138 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~~~~~  138 (145)
                       .. .+.+...|+.+..+|.+.                 +.+..++..++..+...|+.++ +.++++++.+..|++
T Consensus       194 -~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P~~  268 (291)
T 3mkr_A          194 -DK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHRSH  268 (291)
T ss_dssp             -HH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTC
T ss_pred             -Hh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCC
Confidence             21 223444555555544444                 2234455555555555555543 345555555555544

>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=2e-08  Score=61.67  Aligned_cols=116  Identities=15%  Similarity=0.163  Sum_probs=69.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      .|..+...+.+.|++++|..+|+++.. .. +.+...+..+...+...|+++.|...++.+. ..+ ..+...+..+...
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~-~~~-~~~~~~~~~l~~~   78 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALE-LD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKAL-ELD-PRSAEAWYNLGNA   78 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-HHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHH-cC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHH-HHC-CCchHHHHHHHHH
Confidence            345555555555555555555555543 22 1234455555555555555555555555555 211 2234444444444


Q ss_pred             HhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           98 LATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        98 ~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      |.+.                 +.+..++..+...+...|++++|...++++.+..|+
T Consensus        79 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~  135 (136)
T 2fo7_A           79 YYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR  135 (136)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHccCCC
Confidence            4443                 335667888889999999999999999988776664

>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=98.97  E-value=4.1e-09  Score=78.13  Aligned_cols=134  Identities=12%  Similarity=0.094  Sum_probs=72.6

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +|.++|+.+.   +.+..+|..+..++.+.|++++|...|+.+.+ .+ +.+...+..+..++.+.|+++.|...|+.+.
T Consensus        44 ~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  121 (450)
T 2y4t_A           44 DALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQ-LK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVL  121 (450)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-cC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4555555432   22445555555555555555555555555544 22 1134455555555555555555555555554


Q ss_pred             hhcC-----------------------------------------------c-CccHHHHHHHHHHHhcC----------
Q 047113           80 HDFQ-----------------------------------------------L-DLNLEHYGITVDLLATG----------  101 (145)
Q Consensus        80 ~~~~-----------------------------------------------~-~~~~~~~~~li~~~~~~----------  101 (145)
                       ...                                               . +.+...+..+..+|.+.          
T Consensus       122 -~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  200 (450)
T 2y4t_A          122 -KSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDL  200 (450)
T ss_dssp             -TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHH
T ss_pred             -hcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHH
Confidence             111                                               1 12344455555555544          


Q ss_pred             -------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113          102 -------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       102 -------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                             +.+..+|..+...|...|++++|...++++.+..|+++
T Consensus       201 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  245 (450)
T 2y4t_A          201 KAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHK  245 (450)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCChH
Confidence                   44566777777777777777777777777766666544

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=98.97  E-value=6.1e-09  Score=71.54  Aligned_cols=137  Identities=9%  Similarity=0.007  Sum_probs=112.1

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|++..   +.+...|..+...+.+.|++++|...|+++.. .+..| +...+..+...+.+.|+++.|...++.
T Consensus        88 ~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  166 (252)
T 2ho1_A           88 KLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEEAYQRLLEASQ-DTLYPERSRVFENLGLVSLQMKKPAQAKEYFEK  166 (252)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT-CTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHh-CccCcccHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            46777777653   34678899999999999999999999999866 55566 567888999999999999999999999


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      .. ... ..+...+..+..+|.+.                 +.+...+..+...+...|++++|...++++.+..|+++.
T Consensus       167 ~~-~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~~~~  244 (252)
T 2ho1_A          167 SL-RLN-RNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYPGSLE  244 (252)
T ss_dssp             HH-HHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSHH
T ss_pred             HH-hcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCHH
Confidence            88 332 23577788888888766                 446678888999999999999999999999888887654


Q ss_pred             C
Q 047113          141 Y  141 (145)
Q Consensus       141 ~  141 (145)
                      .
T Consensus       245 ~  245 (252)
T 2ho1_A          245 Y  245 (252)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.96  E-value=7.4e-09  Score=69.50  Aligned_cols=135  Identities=10%  Similarity=-0.080  Sum_probs=97.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhcc-chHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYS-GLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~-~~~~~a~~~~~~   77 (145)
                      ++|.+.|+...   +.+...|..+...+...|++++|...|+.... .. +.+...+..+...+... |+++.|...++.
T Consensus        25 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~  102 (225)
T 2vq2_A           25 RQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALS-IK-PDSAEINNNYGWFLCGRLNRPAESMAYFDK  102 (225)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHH-hC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            45667776543   33567888888888888888888888888765 32 23567788888888888 888888888888


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC-CC
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP-KN  138 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~  138 (145)
                      +. ..+..| +...+..+..+|.+.                 +.+...+..+...+...|++++|...+++..+..| ++
T Consensus       103 ~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~  181 (225)
T 2vq2_A          103 AL-ADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQ  181 (225)
T ss_dssp             HH-TSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCC
T ss_pred             HH-cCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCC
Confidence            88 433333 366677777777665                 33466777888888888888888888887776665 44


Q ss_pred             C
Q 047113          139 D  139 (145)
Q Consensus       139 ~  139 (145)
                      +
T Consensus       182 ~  182 (225)
T 2vq2_A          182 A  182 (225)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.96  E-value=6.1e-09  Score=68.59  Aligned_cols=134  Identities=12%  Similarity=0.013  Sum_probs=83.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|++.-   +.+...|..+...+.+.|++++|...+..... .. +-+...+..+-..+...++++.+...+...
T Consensus        22 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a   99 (184)
T 3vtx_A           22 DGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVV-LD-TTSAEAYYILGSANFMIDEKQAAIDALQRA   99 (184)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-cC-chhHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45666666442   23556677777777777777777777766544 22 124455555666666667777777766666


Q ss_pred             hhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           79 VHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      . .  ..| +...+..+..+|.+.                 +.+..+|..+-..|.+.|++++|...|++..+.+|+++.
T Consensus       100 ~-~--~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~a~  176 (184)
T 3vtx_A          100 I-A--LNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKYFKKALEKEEKKAK  176 (184)
T ss_dssp             H-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTHHHHH
T ss_pred             H-H--hCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhCCccCHH
Confidence            5 2  222 455566666666554                 345567777777777778888888877777777765543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.94  E-value=5e-09  Score=74.78  Aligned_cols=131  Identities=12%  Similarity=-0.008  Sum_probs=100.6

Q ss_pred             chHHHHhccCC----CC-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGII----DK-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~----~~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|+++-    .| +...+..+-.++.+.|++++|++.|++       ..+...+..+...+.+.|+++.|...++
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~-------~~~~~~~~~l~~~~~~~g~~~~A~~~l~  154 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ-------GDSLECMAMTVQILLKLDRLDLARKELK  154 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT-------CCSHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            46777887652    24 556677777899999999999999975       3577889999999999999999999999


Q ss_pred             HhhhhcCcCccHH---HHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           77 IMVHDFQLDLNLE---HYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        77 ~m~~~~~~~~~~~---~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .+. ..  .|+..   ...+++..+...                 +.+...|+.+..++.+.|++++|...+++..+..|
T Consensus       155 ~~~-~~--~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p  231 (291)
T 3mkr_A          155 KMQ-DQ--DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDS  231 (291)
T ss_dssp             HHH-HH--CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHH-hh--CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            998 33  35432   112233333221                 55778999999999999999999999999999999


Q ss_pred             CCCCCc
Q 047113          137 KNDAYY  142 (145)
Q Consensus       137 ~~~~~~  142 (145)
                      +++..+
T Consensus       232 ~~~~~l  237 (291)
T 3mkr_A          232 GHPETL  237 (291)
T ss_dssp             TCHHHH
T ss_pred             CCHHHH
Confidence            877544

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.94  E-value=2.1e-09  Score=77.96  Aligned_cols=137  Identities=8%  Similarity=0.047  Sum_probs=83.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+.+.   +.+..+|..+...+.+.|++++|...|++... .. +.+...+..+...+...|+++.|...++++
T Consensus        82 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  159 (365)
T 4eqf_A           82 PVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLE-LQ-PNNLKALMALAVSYTNTSHQQDACEALKNW  159 (365)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHccccHHHHHHHHHHH
Confidence            45666666542   23556677777777777777777777776654 22 224566666666677777766666666665


Q ss_pred             hhhc-----------------------------------------CcCc---cHHHHHHHHHHHhcC-------------
Q 047113           79 VHDF-----------------------------------------QLDL---NLEHYGITVDLLATG-------------  101 (145)
Q Consensus        79 ~~~~-----------------------------------------~~~~---~~~~~~~li~~~~~~-------------  101 (145)
                      ....                                         ...|   +..+|..+...|.+.             
T Consensus       160 l~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  239 (365)
T 4eqf_A          160 IKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAA  239 (365)
T ss_dssp             HHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            5210                                         0011   455666666666554             


Q ss_pred             ----CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113          102 ----ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus       102 ----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                          +.+..+|+.+..+|...|++++|...+++..+..|+++.
T Consensus       240 l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~  282 (365)
T 4eqf_A          240 LTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIR  282 (365)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchH
Confidence                334567777777777777777777777776666665543

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.94  E-value=1e-08  Score=67.51  Aligned_cols=123  Identities=15%  Similarity=0.084  Sum_probs=100.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      ++.+|..|-..|.+.|++++|+..|++..+ .  .| +...+..+-..+.+.|+++.|...+.... ... ..+...+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~-~--~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~-~~~-~~~~~~~~~   78 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLK-A--DPNNVETLLKLGKTYMDIGLPNDAIESLKKFV-VLD-TTSAEAYYI   78 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHC-CCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-hcC-chhHHHHHH
Confidence            567899999999999999999999999876 3  45 67789999999999999999999999987 322 223555555


Q ss_pred             HHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           94 TVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        94 li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      +...+...                 +.+...+..+-..|.+.|++++|...+++..+..|+++..+
T Consensus        79 ~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~  144 (184)
T 3vtx_A           79 LGSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAY  144 (184)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHH
Confidence            55555544                 44677899999999999999999999999999999876554

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.92  E-value=1e-08  Score=69.78  Aligned_cols=133  Identities=10%  Similarity=0.011  Sum_probs=77.1

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +|.+.|+...   +.+...|..+...+.+.|++++|...|++..+ .. +.+...+..+...+.+.|+++.|...++...
T Consensus        75 ~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~  152 (243)
T 2q7f_A           75 RALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALR-AG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAV  152 (243)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            4445554332   23455666666666666666666666666554 22 2245556666666666666666666666665


Q ss_pred             hhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           80 HDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                       ... ..+...+..+..+|.+.                 +.+..+|..+...|...|++++|...++++.+..|+++
T Consensus       153 -~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~  227 (243)
T 2q7f_A          153 -ELN-ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHM  227 (243)
T ss_dssp             -HHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTTCH
T ss_pred             -HhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcchH
Confidence             211 22344555555555443                 33455677777777777777777777777766666554

>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=98.90  E-value=3e-08  Score=70.21  Aligned_cols=138  Identities=8%  Similarity=-0.069  Sum_probs=93.3

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|++... .. +.+...+..+...+...|++++|...++..
T Consensus       142 ~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  219 (330)
T 3hym_B          142 DQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALS-IA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDA  219 (330)
T ss_dssp             HHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHT-TC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHH-hC-CCChHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            34555555442   22445666677777777777777777777654 22 235667777777888888888888888777


Q ss_pred             hhhcC-------cCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           79 VHDFQ-------LDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        79 ~~~~~-------~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      .....       ...+...|..+..+|.+.                 +.+..+|..+...|...|++++|...+++..+.
T Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  299 (330)
T 3hym_B          220 LEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGL  299 (330)
T ss_dssp             HHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT
T ss_pred             HHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHcc
Confidence            63210       123356777777777665                 445667888888888888888888888888888


Q ss_pred             CCCCCCC
Q 047113          135 DPKNDAY  141 (145)
Q Consensus       135 ~~~~~~~  141 (145)
                      .|+++..
T Consensus       300 ~p~~~~~  306 (330)
T 3hym_B          300 RRDDTFS  306 (330)
T ss_dssp             CSCCHHH
T ss_pred             CCCchHH
Confidence            8766543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.89  E-value=1.7e-08  Score=68.74  Aligned_cols=135  Identities=14%  Similarity=0.026  Sum_probs=109.0

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhcc-----------c
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYS-----------G   66 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~-----------~   66 (145)
                      ++|...|+..   .+.+...|..+-.++.+.|++++|...|++..+ .  .| +...+..+-..+.+.           |
T Consensus        22 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g   98 (217)
T 2pl2_A           22 DAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVA-R--TPRYLGGYMVLSEAYVALYRQAEDRERGKG   98 (217)
T ss_dssp             HHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHHHTCSSHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCCcHHHHHHHHHHHHHhhhhhhhhccccc
Confidence            5677888854   334678899999999999999999999999866 3  45 567888888889999           9


Q ss_pred             hHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHc
Q 047113           67 LIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        67 ~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      ++++|...+++.. +  +.| +...|..+..+|.+.                ..+...|..+-..|...|++++|...++
T Consensus        99 ~~~~A~~~~~~al-~--~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  175 (217)
T 2pl2_A           99 YLEQALSVLKDAE-R--VNPRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALAELYLSMGRLDEALAQYA  175 (217)
T ss_dssp             HHHHHHHHHHHHH-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH-H--hCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999999988 3  345 467777777777765                3456788889999999999999999999


Q ss_pred             cCCCCCCCCCCCc
Q 047113          130 DPFHLDPKNDAYY  142 (145)
Q Consensus       130 ~~~~~~~~~~~~~  142 (145)
                      +..+..|+++..+
T Consensus       176 ~al~~~P~~~~~~  188 (217)
T 2pl2_A          176 KALEQAPKDLDLR  188 (217)
T ss_dssp             HHHHHSTTCHHHH
T ss_pred             HHHHhCCCChHHH
Confidence            9988888776543

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.87  E-value=1.5e-08  Score=68.97  Aligned_cols=135  Identities=10%  Similarity=0.021  Sum_probs=107.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...|++..   +.+...|..+...+.+.|++++|...|++... .. +.+...+..+...+...|+++.|...++..
T Consensus        40 ~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  117 (243)
T 2q7f_A           40 EKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALE-LD-SSAATAYYGAGNVYVVKEMYKEAKDMFEKA  117 (243)
T ss_dssp             --CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-cC-CcchHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            45556666542   34678899999999999999999999999876 33 336788899999999999999999999999


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      . +.. ..+...+..+...|.+.                 +.+...+..+...+...|++++|...+++..+..|+++.
T Consensus       118 ~-~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~  194 (243)
T 2q7f_A          118 L-RAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHAD  194 (243)
T ss_dssp             H-HHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHH
T ss_pred             H-HhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHH
Confidence            8 322 33567788888877766                 446778999999999999999999999998887776544

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.86  E-value=6.9e-09  Score=75.17  Aligned_cols=122  Identities=8%  Similarity=-0.044  Sum_probs=95.2

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +...|..+...+.+.|++++|...|+++.. .. +.+...|..+...+.+.|+++.|...|++.. ... +.+...|..+
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~~~-p~~~~~~~~l  139 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAIL-QD-PGDAEAWQFLGITQAENENEQAAIVALQRCL-ELQ-PNNLKALMAL  139 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHC-TTCHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHH-hC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-hcC-CCCHHHHHHH
Confidence            566799999999999999999999999876 33 3378899999999999999999999999998 322 2357788888


Q ss_pred             HHHHhcC------------------------------------------------------------CC---chhhHHHH
Q 047113           95 VDLLATG------------------------------------------------------------ET---EPYVWGAL  111 (145)
Q Consensus        95 i~~~~~~------------------------------------------------------------~p---~~~~~~~l  111 (145)
                      ..+|.+.                                                            .|   +..+|..+
T Consensus       140 ~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  219 (365)
T 4eqf_A          140 AVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGL  219 (365)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHH
T ss_pred             HHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHH
Confidence            8888766                                                            11   45566777


Q ss_pred             HHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113          112 LGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus       112 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ...|...|++++|...+++..+..|+++.
T Consensus       220 ~~~~~~~g~~~~A~~~~~~al~~~p~~~~  248 (365)
T 4eqf_A          220 GVLFHLSGEFNRAIDAFNAALTVRPEDYS  248 (365)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHH
Confidence            77777777777777777776666665543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.85  E-value=3.1e-08  Score=66.38  Aligned_cols=137  Identities=9%  Similarity=-0.053  Sum_probs=110.7

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHc-CChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIH-GQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~-g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|+...   +.+..+|..+...+... |++++|...|+.+.. .+..|+ ...+..+...+...|+++.|...++
T Consensus        59 ~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  137 (225)
T 2vq2_A           59 DKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGLAEAYLK  137 (225)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            46777777553   34677899999999999 999999999999876 545554 6788999999999999999999999


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcC-----------------C-CchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATG-----------------E-TEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~-----------------~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      .+. ... +.+...+..+..+|.+.                 + .+...+..+...+...|+.+++...++.+.+..|++
T Consensus       138 ~~~-~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p~~  215 (225)
T 2vq2_A          138 RSL-AAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFPYS  215 (225)
T ss_dssp             HHH-HHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHH-HhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC
Confidence            998 322 23477788888877765                 4 567788888888899999999999999988888876


Q ss_pred             CCC
Q 047113          139 DAY  141 (145)
Q Consensus       139 ~~~  141 (145)
                      +..
T Consensus       216 ~~~  218 (225)
T 2vq2_A          216 EEL  218 (225)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>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=98.81  E-value=6.5e-08  Score=68.42  Aligned_cols=136  Identities=13%  Similarity=0.092  Sum_probs=89.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|++... .. +.+...+..+...+...|+++.|...++..
T Consensus       108 ~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  185 (330)
T 3hym_B          108 EHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQ-LM-KGCHLPMLYIGLEYGLTNNSKLAERFFSQA  185 (330)
T ss_dssp             HHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HT-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHH-hc-cccHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            34666666442   23456677777777777777777777777655 32 223455666777777777777777777777


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC----------------C---------Cc-hhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG----------------E---------TE-PYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~----------------~---------p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      . ... +.+...+..+...|.+.                .         |+ ..+|..+...|...|++++|...+++..
T Consensus       186 l-~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  263 (330)
T 3hym_B          186 L-SIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQAL  263 (330)
T ss_dssp             H-TTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             H-HhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            6 221 23466666776666655                0         32 3577777788888888888888888777


Q ss_pred             CCCCCCCCC
Q 047113          133 HLDPKNDAY  141 (145)
Q Consensus       133 ~~~~~~~~~  141 (145)
                      +..|+++..
T Consensus       264 ~~~~~~~~~  272 (330)
T 3hym_B          264 VLIPQNAST  272 (330)
T ss_dssp             HHSTTCSHH
T ss_pred             hhCccchHH
Confidence            766665543

>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=98.80  E-value=1.7e-08  Score=72.76  Aligned_cols=76  Identities=14%  Similarity=0.239  Sum_probs=52.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...|+.+.   +.+...|..+..++.+.|++++|...|++... .. +.+..++..+...+...|+++.|...++.+
T Consensus        81 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  158 (368)
T 1fch_A           81 PNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLE-LK-PDNQTALMALAVSFTNESLQRQACEILRDW  158 (368)
T ss_dssp             HHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45666676553   23566777777777788888888888777765 33 235667777777777777777777777766


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       159 ~  159 (368)
T 1fch_A          159 L  159 (368)
T ss_dssp             H
T ss_pred             H
Confidence            5

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.78  E-value=2.2e-08  Score=79.91  Aligned_cols=120  Identities=10%  Similarity=0.068  Sum_probs=73.9

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGI   93 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~   93 (145)
                      ...|+.|-.++.+.|++++|+..|++..+   +.| +...|+.+-.++.+.|++++|...|++.. +  +.| +...|..
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~---l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al-~--l~P~~~~a~~n   82 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALE---VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAI-R--ISPTFADAYSN   82 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCCCCHHHHHH
Confidence            45666666666666666666666666544   234 35566666666666666666666666665 2  334 3555666


Q ss_pred             HHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           94 TVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        94 li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +..+|.+.                .| +...|+.+-.+|.+.|++++|+..+++..+++|+++..
T Consensus        83 Lg~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a  147 (723)
T 4gyw_A           83 MGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDA  147 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHH
Confidence            66655554                33 44566666677777777777777777766666655443

>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=98.76  E-value=1.2e-08  Score=65.78  Aligned_cols=120  Identities=8%  Similarity=-0.057  Sum_probs=95.1

Q ss_pred             chHHHHhccCCC--C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|....+  | +...|-.+-..|.+.|++++|...|+...+   +.| +...|..+-.++.+.|+++.|...|+.
T Consensus        14 e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~---~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~   90 (150)
T 4ga2_A           14 ERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYIN---VQERDPKAHRFLGLLYELEENTDKAVECYRR   90 (150)
T ss_dssp             HHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCchHHHHHHHHH
Confidence            567777776544  2 455677888999999999999999999876   345 678999999999999999999999999


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHH-HccCCCCCCCCCCCcc
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELV-AKDPFHLDPKNDAYYT  143 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~-~~~~~~~~~~~~~~~~  143 (145)
                      .. +  +.|+                +...|..+-..|.+.|+.++|... +++..++.|+++..|.
T Consensus        91 al-~--~~p~----------------~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~  138 (150)
T 4ga2_A           91 SV-E--LNPT----------------QKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYK  138 (150)
T ss_dssp             HH-H--HCTT----------------CHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHH
T ss_pred             HH-H--hCCC----------------CHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHH
Confidence            88 3  3443                566777788888999998776554 5888888998876553

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.74  E-value=2.3e-08  Score=68.36  Aligned_cols=65  Identities=14%  Similarity=0.181  Sum_probs=36.1

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC--CCCc----HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSD--GKPN----NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~--~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ++...|..+..++.+.|++++|...|+.... ..  ..|+    ...+..+...+...|+++.|...++...
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  106 (258)
T 3uq3_A           36 KDITYLNNRAAAEYEKGEYETAISTLNDAVE-QGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSL  106 (258)
T ss_dssp             CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcccHHHHHHHHHHHHH-hCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            4455566666666666666666666665443 11  0011    3555566666666666666666666555

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.74  E-value=3.6e-08  Score=61.81  Aligned_cols=106  Identities=10%  Similarity=0.018  Sum_probs=90.1

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ....|...-..+.+.|++++|+..|++..+ .. +.+...|..+-.++.+.|+++.|...++... +  +.|        
T Consensus        12 ~a~~~~~~G~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al-~--~~p--------   78 (126)
T 4gco_A           12 LAQEEKNKGNEYFKKGDYPTAMRHYNEAVK-RD-PENAILYSNRAACLTKLMEFQRALDDCDTCI-R--LDS--------   78 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCT--------
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHH-H--hhh--------
Confidence            345788999999999999999999999766 33 2368899999999999999999999999988 3  333        


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                              .+...|..+-.+|...|++++|...|++..+++|+++..
T Consensus        79 --------~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~l~P~~~~a  117 (126)
T 4gco_A           79 --------KFIKGYIRKAACLVAMREWSKAQRAYEDALQVDPSNEEA  117 (126)
T ss_dssp             --------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             --------hhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcCCHHH
Confidence                    256678888899999999999999999999999987654

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=98.74  E-value=1.9e-07  Score=65.88  Aligned_cols=130  Identities=5%  Similarity=0.015  Sum_probs=105.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|++... .. +.+...+..+...+...|++++|...++..
T Consensus       155 ~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  232 (327)
T 3cv0_A          155 RECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVE-LR-PDDAQLWNKLGATLANGNRPQEALDAYNRA  232 (327)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH-hC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            46677777653   34678899999999999999999999999876 33 336788999999999999999999999998


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC----------------CC-------------chhhHHHHHHHHHhccChhHHHHHHc
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG----------------ET-------------EPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~----------------~p-------------~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      . ... +.+...|..+..+|.+.                .|             +..+|..+..++.+.|++++|..+++
T Consensus       233 ~-~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  310 (327)
T 3cv0_A          233 L-DIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYA  310 (327)
T ss_dssp             H-HHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTT
T ss_pred             H-HcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            8 322 33577888888888776                33             46789999999999999999999999


Q ss_pred             cCCCCC
Q 047113          130 DPFHLD  135 (145)
Q Consensus       130 ~~~~~~  135 (145)
                      +..+..
T Consensus       311 ~~l~~~  316 (327)
T 3cv0_A          311 QNVEPF  316 (327)
T ss_dssp             CCSHHH
T ss_pred             HHHHhc
Confidence            877643

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.71  E-value=5.7e-08  Score=63.07  Aligned_cols=102  Identities=7%  Similarity=-0.119  Sum_probs=88.2

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      +...|..+-..+.+.|++++|...|+.... .  .| +...|..+-.++...|++++|...|++.. .  +.|+      
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~-~--~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al-~--l~P~------  102 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCI-Y--DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAF-A--LGKN------  102 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HSSS------
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHH-h--hCCC------
Confidence            566889999999999999999999999876 3  45 68889999999999999999999999998 2  4443      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                                +...|..+-.+|...|++++|...|++..+..|+.
T Consensus       103 ----------~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~~~~  137 (151)
T 3gyz_A          103 ----------DYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDE  137 (151)
T ss_dssp             ----------CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCH
T ss_pred             ----------CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCH
Confidence                      66778888899999999999999999988877754

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.71  E-value=1.9e-07  Score=66.52  Aligned_cols=133  Identities=14%  Similarity=0.021  Sum_probs=89.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|+.... .  .| +...+..+...+...|+++.|...++.
T Consensus        20 ~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~   96 (359)
T 3ieg_A           20 ADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIA-L--KMDFTAARLQRGHLLLKQGKLDEAEDDFKK   96 (359)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHH-h--CCCcchHHHHHHHHHHHcCChHHHHHHHHH
Confidence            46677777553   23566788888888888888888888888765 3  34 566778888888888888888888888


Q ss_pred             hhhhcCcCc----cHHHHHHH------------HHHHhcC-----------------CCchhhHHHHHHHHHhccChhHH
Q 047113           78 MVHDFQLDL----NLEHYGIT------------VDLLATG-----------------ETEPYVWGALLGACRIHHNVKIG  124 (145)
Q Consensus        78 m~~~~~~~~----~~~~~~~l------------i~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a  124 (145)
                      .. .  ..|    +...+..+            ...+.+.                 +.+...+..+...+...|++++|
T Consensus        97 ~~-~--~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A  173 (359)
T 3ieg_A           97 VL-K--SNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKA  173 (359)
T ss_dssp             HH-T--SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HH-h--cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHH
Confidence            77 2  234    33344333            2223222                 34556677777777777777777


Q ss_pred             HHHHccCCCCCCCCCC
Q 047113          125 ELVAKDPFHLDPKNDA  140 (145)
Q Consensus       125 ~~~~~~~~~~~~~~~~  140 (145)
                      ...+++..+..|+++.
T Consensus       174 ~~~~~~~~~~~~~~~~  189 (359)
T 3ieg_A          174 ISDLKAASKLKSDNTE  189 (359)
T ss_dssp             HHHHHHHHTTCSCCHH
T ss_pred             HHHHHHHHHhCCCCHH
Confidence            7777777766665543

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.71  E-value=8.2e-08  Score=72.85  Aligned_cols=134  Identities=12%  Similarity=0.098  Sum_probs=110.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhcc---------chHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYS---------GLIE   69 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~---------~~~~   69 (145)
                      ++|.+.|++..   +.+...|..+-.+|.+.|++++|...|+...+   +.|+...+..+-..+...         |+++
T Consensus       120 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~  196 (474)
T 4abn_A          120 PEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALT---HCKNKVSLQNLSMVLRQLQTDSGDEHSRHVM  196 (474)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT---TCCCHHHHHHHHHHHTTCCCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCCCHHHHHHHHHHHHHhccCChhhhhhhHH
Confidence            67888888653   34678999999999999999999999999866   458888899999999999         9999


Q ss_pred             HHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhc-----------C-------------CC----chhhHHHHHHHHHhccC
Q 047113           70 EGIKVFDIMVHDFQLDL-NLEHYGITVDLLAT-----------G-------------ET----EPYVWGALLGACRIHHN  120 (145)
Q Consensus        70 ~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~-----------~-------------~p----~~~~~~~li~~~~~~g~  120 (145)
                      +|...+++.. +  +.| +...|..+..+|.+           .             .|    +...|..+-.+|...|+
T Consensus       197 ~A~~~~~~al-~--~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~  273 (474)
T 4abn_A          197 DSVRQAKLAV-Q--MDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEES  273 (474)
T ss_dssp             HHHHHHHHHH-H--HCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHH-H--hCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCC
Confidence            9999999988 3  344 46777777777642           1             44    67889999999999999


Q ss_pred             hhHHHHHHccCCCCCCCCCCC
Q 047113          121 VKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       121 ~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +++|...|++..+..|+++..
T Consensus       274 ~~~A~~~~~~al~l~p~~~~a  294 (474)
T 4abn_A          274 YGEALEGFSQAAALDPAWPEP  294 (474)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHH
Confidence            999999999999888876543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.70  E-value=1.3e-07  Score=64.31  Aligned_cols=125  Identities=9%  Similarity=-0.054  Sum_probs=89.6

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHc-----------CChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIH-----------GQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG   66 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~-----------g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~   66 (145)
                      ++|...|+..   .+.+...|..+-.++.+.           |++++|...|+...+   +.| +...+..+-..+...|
T Consensus        56 ~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~---~~P~~~~~~~~lg~~~~~~g  132 (217)
T 2pl2_A           56 NPALENGKTLVARTPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAER---VNPRYAPLHLQRGLVYALLG  132 (217)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHcC
Confidence            4677777754   334677899999999999           999999999999866   345 5778888889999999


Q ss_pred             hHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHc
Q 047113           67 LIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        67 ~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      ++++|...|++.. ...  .+...+..+..+|.+.                 +.+...+..+...+...|++++|...++
T Consensus       133 ~~~~A~~~~~~al-~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~  209 (217)
T 2pl2_A          133 ERDKAEASLKQAL-ALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAA  209 (217)
T ss_dssp             CHHHHHHHHHHHH-HHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC------------
T ss_pred             ChHHHHHHHHHHH-hcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHH
Confidence            9999999999998 545  6778888888777665                 4466789999999999999999999988


Q ss_pred             cCC
Q 047113          130 DPF  132 (145)
Q Consensus       130 ~~~  132 (145)
                      +..
T Consensus       210 ~~~  212 (217)
T 2pl2_A          210 LEH  212 (217)
T ss_dssp             ---
T ss_pred             HHh
Confidence            753

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.69  E-value=2.5e-07  Score=63.96  Aligned_cols=133  Identities=12%  Similarity=-0.003  Sum_probs=98.7

Q ss_pred             chHHHHhccCCC-------CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID-------KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~-------~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.+.|+.+..       .+..+|..+...+.+.|++++|...|++... .. +.+...|..+...+...|+++.|...
T Consensus        22 ~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~   99 (275)
T 1xnf_A           22 EVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALA-IR-PDMPEVFNYLGIYLTQAGNFDAAYEA   99 (275)
T ss_dssp             HHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHH-cC-CCcHHHHHHHHHHHHHccCHHHHHHH
Confidence            567777775533       1467899999999999999999999999876 33 23678899999999999999999999


Q ss_pred             HHHhhhhcCcCccHHHHHHHHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           75 FDIMVHDFQLDLNLEHYGITVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        75 ~~~m~~~~~~~~~~~~~~~li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      +++.. ... +.+...|..+..+|.+.                .|+.......+..+...|++++|...+++.....|++
T Consensus       100 ~~~al-~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~  177 (275)
T 1xnf_A          100 FDSVL-ELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKE  177 (275)
T ss_dssp             HHHHH-HHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHH-hcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCcc
Confidence            99998 321 22567777777777766                4554444455555667788888888887766655544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.68  E-value=4.3e-07  Score=54.12  Aligned_cols=108  Identities=17%  Similarity=0.092  Sum_probs=88.0

Q ss_pred             CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           13 DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        13 ~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      +.+...|..+...+.+.|++++|...|++..+ .. +.+...+..+-..+...|+++.|...+++.. ..  .|+     
T Consensus         3 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~-~~--~~~-----   72 (112)
T 2kck_A            3 DQNPEEYYLEGVLQYDAGNYTESIDLFEKAIQ-LD-PEESKYWLMKGKALYNLERYEEAVDCYNYVI-NV--IED-----   72 (112)
T ss_dssp             CSSTTGGGGHHHHHHSSCCHHHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HT--SCC-----
T ss_pred             CCcHHHHHHHHHHHHHhhhHHHHHHHHHHHHH-hC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHH-Hh--Ccc-----
Confidence            34567888999999999999999999999876 33 3367788889999999999999999999988 32  221     


Q ss_pred             HHHHHHhcCCCchhhHHHHHHHHHhc-cChhHHHHHHccCCCCCCCCC
Q 047113           93 ITVDLLATGETEPYVWGALLGACRIH-HNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        93 ~li~~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~~~~~  139 (145)
                               ..+...|..+...+... |++++|.+.+++..+..|+++
T Consensus        73 ---------~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~p~~~  111 (112)
T 2kck_A           73 ---------EYNKDVWAAKADALRYIEGKEVEAEIAEARAKLEHHHHH  111 (112)
T ss_dssp             ---------TTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGGCCCCC
T ss_pred             ---------cchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhcccCCC
Confidence                     01456777788899999 999999999999999888654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.68  E-value=1e-07  Score=57.88  Aligned_cols=104  Identities=18%  Similarity=0.232  Sum_probs=86.9

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|..+...+.+.|++++|...|+++.. .. +.+...+..+...+.+.|+++.|...++.+. ..  .|         
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~-~~--~~---------   74 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALE-LD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKAL-EL--DP---------   74 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CT---------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH-Hh--CC---------
Confidence            56899999999999999999999999876 33 3367788999999999999999999999988 32  22         


Q ss_pred             HHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           96 DLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        96 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                             .+..+|..+...|...|++++|...++++.+..|+++.
T Consensus        75 -------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~  112 (125)
T 1na0_A           75 -------NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAE  112 (125)
T ss_dssp             -------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             -------ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHH
Confidence                   24556777888899999999999999998888776654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.66  E-value=2e-07  Score=63.03  Aligned_cols=131  Identities=9%  Similarity=0.016  Sum_probs=100.4

Q ss_pred             chHHHHhccCCC--C-chhhHHH----------------HHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K-NVVIWSG----------------MIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFA   61 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~~~~~----------------li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~   61 (145)
                      ++|...|+....  | +...|..                +-.++.+.|++++|...|++..+ .  .| +...+..+-..
T Consensus        21 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~--~p~~~~~~~~lg~~   97 (208)
T 3urz_A           21 GQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQ-K--APNNVDCLEACAEM   97 (208)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-H--CCCCHHHHHHHHHH
Confidence            467777776532  3 4556666                89999999999999999999876 3  45 67899999999


Q ss_pred             hhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC----------------CCch--hhHHHHHHHHHhccChh
Q 047113           62 CSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG----------------ETEP--YVWGALLGACRIHHNVK  122 (145)
Q Consensus        62 ~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~~--~~~~~li~~~~~~g~~~  122 (145)
                      +...|+++.|...|++.. .  +.| +...|..+..+|...                .|+.  ..+..+-.++...|+++
T Consensus        98 ~~~~g~~~~A~~~~~~al-~--~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~  174 (208)
T 3urz_A           98 QVCRGQEKDALRMYEKIL-Q--LEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRYE  174 (208)
T ss_dssp             HHHHTCHHHHHHHHHHHH-H--HCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHcCCHHHHHHHHHHHH-H--cCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCHH
Confidence            999999999999999998 3  455 577787777766422                3332  33444455667789999


Q ss_pred             HHHHHHccCCCCCCCC
Q 047113          123 IGELVAKDPFHLDPKN  138 (145)
Q Consensus       123 ~a~~~~~~~~~~~~~~  138 (145)
                      +|...|++..++.|+.
T Consensus       175 ~A~~~~~~al~l~P~~  190 (208)
T 3urz_A          175 KARNSLQKVILRFPST  190 (208)
T ss_dssp             HHHHHHHHHTTTSCCH
T ss_pred             HHHHHHHHHHHhCCCH
Confidence            9999999999998853

>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=98.66  E-value=8.2e-07  Score=59.40  Aligned_cols=131  Identities=15%  Similarity=0.027  Sum_probs=92.6

Q ss_pred             chHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhh
Q 047113            2 DDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus         2 ~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      ++|.+.|++..+++...|..+...+.+.|++++|...|++... .. +.+...+..+-.++...|+++.|...|+.....
T Consensus        23 ~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  100 (213)
T 1hh8_A           23 KGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSIN-RD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQ  100 (213)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-ccchHHHHHHHHHHHHcccHHHHHHHHHHHHHh
Confidence            5688888877777888888899999999999999999988765 33 336678888888888999999999988888721


Q ss_pred             cCcCccHHHHHHHHHHHhcCCC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           82 FQLDLNLEHYGITVDLLATGET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        82 ~~~~~~~~~~~~li~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      ..-.+... |..+.   ....| ....|..+-.+|...|++++|...+++..+..|+.
T Consensus       101 ~~~~~~~~-~~~~~---~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  154 (213)
T 1hh8_A          101 LRGNQLID-YKILG---LQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  154 (213)
T ss_dssp             TTTCSEEE-CGGGT---BCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             CCCccHHH-HHHhc---cccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCccc
Confidence            11110000 00000   00011 33577788888999999999999999888877743

>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=98.65  E-value=4.5e-07  Score=65.26  Aligned_cols=127  Identities=9%  Similarity=0.064  Sum_probs=101.3

Q ss_pred             chHHHHhccCCC--C---chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K---NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~--~---~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|+.+..  |   +..+|..+...+.+.|++++|...|++... .. +.+...+..+...+.+.|+++.|...++
T Consensus       198 ~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  275 (368)
T 1fch_A          198 LEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALS-VR-PNDYLLWNKLGATLANGNQSEEAVAAYR  275 (368)
T ss_dssp             HHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-cCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            467777776532  3   477899999999999999999999999876 32 3357899999999999999999999999


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcC-----------------CCc-----------hhhHHHHHHHHHhccChhHHHHHH
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATG-----------------ETE-----------PYVWGALLGACRIHHNVKIGELVA  128 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~-----------~~~~~~li~~~~~~g~~~~a~~~~  128 (145)
                      ... ... +.+...+..+..+|.+.                 +.+           ..+|..+..+|...|+.++|..++
T Consensus       276 ~al-~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  353 (368)
T 1fch_A          276 RAL-ELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAAD  353 (368)
T ss_dssp             HHH-HHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHH
T ss_pred             HHH-HhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhH
Confidence            988 321 23577788888888766                 222           578999999999999999999988


Q ss_pred             ccCC
Q 047113          129 KDPF  132 (145)
Q Consensus       129 ~~~~  132 (145)
                      ++..
T Consensus       354 ~~~l  357 (368)
T 1fch_A          354 ARDL  357 (368)
T ss_dssp             TTCH
T ss_pred             HHHH
Confidence            8644

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.65  E-value=2.3e-07  Score=64.08  Aligned_cols=134  Identities=16%  Similarity=-0.011  Sum_probs=92.0

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|+.... .. +.+...+..+...+.+.|++++|...++.+
T Consensus        60 ~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  137 (275)
T 1xnf_A           60 ALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLE-LD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAF  137 (275)
T ss_dssp             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHh-cC-ccccHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            45666676542   34577888888888888888888888888765 32 225677788888888888888888888887


Q ss_pred             hhhcCcCccHHHHHH---------------------------------HHHHHhcC----------------CC-----c
Q 047113           79 VHDFQLDLNLEHYGI---------------------------------TVDLLATG----------------ET-----E  104 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~---------------------------------li~~~~~~----------------~p-----~  104 (145)
                      . +  ..|+......                                 ++..+...                .|     +
T Consensus       138 ~-~--~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  214 (275)
T 1xnf_A          138 Y-Q--DDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHL  214 (275)
T ss_dssp             H-H--HCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHH
T ss_pred             H-H--hCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhcCHHHHHHHHHHHhcccccccccc
Confidence            7 2  2232221111                                 11111111                11     2


Q ss_pred             hhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113          105 PYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus       105 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ..+|..+...|.+.|++++|...+++..+..|++..
T Consensus       215 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~  250 (275)
T 1xnf_A          215 SETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFV  250 (275)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTCH
T ss_pred             cHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchhHH
Confidence            578889999999999999999999999998886543

>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=98.65  E-value=9.4e-08  Score=72.21  Aligned_cols=134  Identities=10%  Similarity=0.038  Sum_probs=88.0

Q ss_pred             chHHHHhccCCC--C-c-------hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHH
Q 047113            2 DDAERIFGGIID--K-N-------VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEG   71 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~-------~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a   71 (145)
                      ++|.++|+.+..  | +       ..+|..+...+...|++++|...|+.... .  .|+...+..+...+...|+++.|
T Consensus       219 ~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~-~--~~~~~~~~~l~~~~~~~~~~~~A  295 (537)
T 3fp2_A          219 TKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESIN-L--HPTPNSYIFLALTLADKENSQEF  295 (537)
T ss_dssp             HHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CCCHHHHHHHHHHTCCSSCCHHH
T ss_pred             HHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHh-c--CCCchHHHHHHHHHHHhcCHHHH
Confidence            356666665533  2 2       22466666777777888888888887765 2  45566777777778888888888


Q ss_pred             HHHHHHhhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           72 IKVFDIMVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        72 ~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      ...++... ... +.+..+|..+...|.+.                 +.+...|..+...|...|++++|...++++.+.
T Consensus       296 ~~~~~~~~-~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  373 (537)
T 3fp2_A          296 FKFFQKAV-DLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLK  373 (537)
T ss_dssp             HHHHHHHH-HHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-ccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            88888777 222 22466677777666655                 334456777777777777777777777776666


Q ss_pred             CCCCCC
Q 047113          135 DPKNDA  140 (145)
Q Consensus       135 ~~~~~~  140 (145)
                      .|+++.
T Consensus       374 ~~~~~~  379 (537)
T 3fp2_A          374 FPTLPE  379 (537)
T ss_dssp             CTTCTH
T ss_pred             CCCChH
Confidence            665543

>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=98.65  E-value=1.3e-08  Score=76.63  Aligned_cols=96  Identities=14%  Similarity=0.187  Sum_probs=31.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ..+.+.|+.+|.+.|+++++.++++        .|+..+|+.+.+.|...|.+++|..+|..+.          .|..|+
T Consensus        94 ~~i~~~Li~~Y~Klg~l~e~e~f~~--------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a~----------n~~~LA  155 (449)
T 1b89_A           94 SYVETELIFALAKTNRLAELEEFIN--------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS----------NFGRLA  155 (449)
T ss_dssp             ---------------CHHHHTTTTT--------CC----------------CTTTHHHHHHHTT----------CHHHHH
T ss_pred             chhHHHHHHHHHHhCCHHHHHHHHc--------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHhh----------hHHHHH
Confidence            3444555555555555555444442        2444455555555555555555555555442          233344


Q ss_pred             HHHhcC------------CCchhhHHHHHHHHHhccChhHHHHHHc
Q 047113           96 DLLATG------------ETEPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        96 ~~~~~~------------~p~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      +++.+.            -.+..+|..++.+|...|+++.|.....
T Consensus       156 ~~L~~Lg~yq~AVea~~KA~~~~~Wk~v~~aCv~~~ef~lA~~~~l  201 (449)
T 1b89_A          156 STLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGL  201 (449)
T ss_dssp             HHHHTTTCHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHTTT
T ss_pred             HHHHHhccHHHHHHHHHHcCCchhHHHHHHHHHHcCcHHHHHHHHH
Confidence            444333            2245556666666665555555544333

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=98.63  E-value=9.8e-08  Score=67.43  Aligned_cols=76  Identities=9%  Similarity=0.104  Sum_probs=53.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.++|+.+.   +.+...|..+..++.+.|++++|...|++..+ .. +.+...+..+...+...|+++.|...++..
T Consensus        38 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  115 (327)
T 3cv0_A           38 AEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARM-LD-PKDIAVHAALAVSHTNEHNANAALASLRAW  115 (327)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-cC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            46777777653   23566777788888888888888888887765 32 235667777777777777777777777766


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       116 ~  116 (327)
T 3cv0_A          116 L  116 (327)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=98.63  E-value=5.1e-07  Score=69.60  Aligned_cols=137  Identities=10%  Similarity=-0.009  Sum_probs=103.7

Q ss_pred             CchHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            1 MDDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         1 ~~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      +++|.+.|++...   .+...|..+-..+.+.|++++|...|++..+   ..| +...+..+-..+.+.|++++|...++
T Consensus         5 ~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~   81 (568)
T 2vsy_A            5 GPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLA---LHPGHPEAVARLGRVRWTQQRHAEAAVLLQ   81 (568)
T ss_dssp             ----------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT---TSTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            3678888886643   3577899999999999999999999999865   345 57789999999999999999999999


Q ss_pred             HhhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhc---cChhHHHHHHccCCCCC
Q 047113           77 IMVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIH---HNVKIGELVAKDPFHLD  135 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~---g~~~~a~~~~~~~~~~~  135 (145)
                      +.. .  ..| +...|..+..+|.+.                 +.+...+..+...+...   |+.++|...+++..+..
T Consensus        82 ~al-~--~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~~  158 (568)
T 2vsy_A           82 QAS-D--AAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQG  158 (568)
T ss_dssp             HHH-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHT
T ss_pred             HHH-h--cCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhcC
Confidence            998 3  234 577888888888776                 44567889999999999   99999999999998888


Q ss_pred             CCCCCCcc
Q 047113          136 PKNDAYYT  143 (145)
Q Consensus       136 ~~~~~~~~  143 (145)
                      |.....+.
T Consensus       159 p~~~~~~~  166 (568)
T 2vsy_A          159 VGAVEPFA  166 (568)
T ss_dssp             CCCSCHHH
T ss_pred             CcccChHH
Confidence            86655443

>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=98.62  E-value=5e-07  Score=61.30  Aligned_cols=119  Identities=11%  Similarity=-0.024  Sum_probs=79.9

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~   93 (145)
                      |...|..+-..+.+.|++++|...|+.... ..-.++...+..+-.++...|++++|...++... .  ..| +...|..
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~-~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al-~--~~p~~~~~~~~   81 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLK-LTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAI-K--KNYNLANAYIG   81 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--TTCSHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHh-ccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHH-H--hCcchHHHHHH
Confidence            445666666667777777777777776655 3322455555556666677777777777777666 2  233 4555666


Q ss_pred             HHHHHhcC----------------CC-ch-------hhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           94 TVDLLATG----------------ET-EP-------YVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        94 li~~~~~~----------------~p-~~-------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      +..+|.+.                .| +.       ..|..+-..+...|++++|...+++..+..|+
T Consensus        82 l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~  149 (228)
T 4i17_A           82 KSAAYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSK  149 (228)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCC
Confidence            66666555                23 33       45777778888999999999999999988886

>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=98.62  E-value=1.9e-07  Score=60.01  Aligned_cols=106  Identities=12%  Similarity=0.016  Sum_probs=87.7

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +...|..+-..+.+.|++++|...|+.... .. +.+...|..+-.++...|++++|...|++.. .  +.|+       
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--l~p~-------   87 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCV-LD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGA-V--MDIX-------   87 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HSTT-------
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHH-cC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHH-h--cCCC-------
Confidence            566788899999999999999999999865 32 2377788889999999999999999999988 3  2332       


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                               +...|..+-.+|...|++++|...|++..+..|+++..
T Consensus        88 ---------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~  125 (148)
T 2vgx_A           88 ---------EPRFPFHAAECLLQXGELAEAESGLFLAQELIANXPEF  125 (148)
T ss_dssp             ---------CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCGGG
T ss_pred             ---------CchHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCCcc
Confidence                     55677778888999999999999999988887766543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.62  E-value=3e-07  Score=68.91  Aligned_cols=62  Identities=5%  Similarity=-0.048  Sum_probs=28.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ...|..+...+.+.|++++|...|+.+.. .. +.+...+..+...+.+.|+++.|...++.+.
T Consensus       338 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  399 (514)
T 2gw1_A          338 IFPYIQLACLAYRENKFDDCETLFSEAKR-KF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAI  399 (514)
T ss_dssp             SHHHHHHHHHTTTTTCHHHHHHHHHHHHH-HS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-Hc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34444444444455555555555544433 11 1133344444444555555555555554444

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.61  E-value=8.4e-07  Score=63.19  Aligned_cols=123  Identities=6%  Similarity=-0.052  Sum_probs=66.2

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHH------------HHHHHhhccchHHHHHHHHHHhhhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFL------------SILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~------------~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      +...|..+...+.+.|++++|...|+...+ .  .| +...+.            .+...+.+.|++++|...++.....
T Consensus       187 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~-~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  263 (359)
T 3ieg_A          187 NTEAFYKISTLYYQLGDHELSLSEVRECLK-L--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT  263 (359)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-h--CccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            444555555555555666666665555543 1  12 222222            1133455556666666666655521


Q ss_pred             cCcCccH--HHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           82 FQLDLNL--EHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        82 ~~~~~~~--~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ..-.+..  ..+..+..+|.+.                 +.+..+|..+...|...|++++|...+++..+..|+++.
T Consensus       264 ~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~~~  341 (359)
T 3ieg_A          264 EPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQ  341 (359)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHH
T ss_pred             CCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChH
Confidence            1111110  1223344444443                 335667777888888888888888888887777776554

>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=98.60  E-value=1.5e-07  Score=71.04  Aligned_cols=137  Identities=12%  Similarity=-0.043  Sum_probs=108.9

Q ss_pred             chHHHHhccCC--CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            2 DDAERIFGGII--DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         2 ~~A~~~f~~m~--~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ++|.+.|+...  .|+...|..+...+.+.|++++|...|+.... .. +.+...+..+...+...|+++.|...++...
T Consensus       260 ~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  337 (537)
T 3fp2_A          260 LDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVD-LN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQ  337 (537)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhc-cC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            46677777553  35677899999999999999999999999876 33 2367789999999999999999999999998


Q ss_pred             hhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           80 HDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                       ... +.+...|..+..+|.+.                 +.+...|..+...+...|++++|...++++.+..|+++..+
T Consensus       338 -~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~  415 (537)
T 3fp2_A          338 -SLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIH  415 (537)
T ss_dssp             -HHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCS
T ss_pred             -HhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhH
Confidence             322 22467788888887766                 44567899999999999999999999999888666555443

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.60  E-value=6.9e-08  Score=66.00  Aligned_cols=131  Identities=8%  Similarity=-0.039  Sum_probs=102.0

Q ss_pred             chHHHHhccCCC--C-c-------hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC------------------------
Q 047113            2 DDAERIFGGIID--K-N-------VVIWSGMIASHAIHGQEREALEAFYLVIHCSD------------------------   47 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~-------~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~------------------------   47 (145)
                      ++|.+.|+....  | +       ...|..+...+.+.|++++|...|+.... ..                        
T Consensus        55 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~~~a~~~~~~~~~  133 (258)
T 3uq3_A           55 ETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLT-EHRTADILTKLRNAEKELKKAEAEAY  133 (258)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHh-cCchhHHHHHHhHHHHHHHHHHHHHH
Confidence            456666665432  1 1       57899999999999999999999999865 32                        


Q ss_pred             CCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC-----------------CCchhhHH
Q 047113           48 GKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG-----------------ETEPYVWG  109 (145)
Q Consensus        48 ~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-----------------~p~~~~~~  109 (145)
                      ..| +...+..+...+...|+++.|...++... ... +.+...|..+..+|.+.                 +.+..+|.
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~-~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~  211 (258)
T 3uq3_A          134 VNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMI-KRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYI  211 (258)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             cCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHH-hcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHH
Confidence            344 45577888888999999999999999988 322 33577788888888766                 44567888


Q ss_pred             HHHHHHHhccChhHHHHHHccCCCCC
Q 047113          110 ALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus       110 ~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      .+...+...|++++|...+++..+..
T Consensus       212 ~l~~~~~~~g~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          212 RKATAQIAVKEYASALETLDAARTKD  237 (258)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            99999999999999999999887765

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.60  E-value=2.6e-07  Score=59.77  Aligned_cols=121  Identities=16%  Similarity=0.011  Sum_probs=98.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|..+...+.+.|++++|...|+++.. .. +.+...+..+...+...|+++.|...++... ... +.+...+..+.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~-~~~-~~~~~~~~~~a   83 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYD-AD-AFDVDVALHLGIAYVKTGAVDRGTELLERSL-ADA-PDNVKVATVLG   83 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCC-TT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHH-hC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHH-hcC-CCCHHHHHHHH
Confidence            35688889999999999999999999854 22 3367888999999999999999999999998 322 33567777777


Q ss_pred             HHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           96 DLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        96 ~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ..|...                 +.+...+..+...+...|++++|...+++..+..|+++.
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~  145 (186)
T 3as5_A           84 LTYVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGK  145 (186)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchH
Confidence            777654                 556778999999999999999999999998887776543

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.59  E-value=4.5e-07  Score=72.39  Aligned_cols=126  Identities=10%  Similarity=0.076  Sum_probs=107.5

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|++.   .+.+...|+.|-.++.+.|++++|+..|++..+   +.| +...|+.+-.++.+.|++++|.+.|++
T Consensus        26 ~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~---l~P~~~~a~~nLg~~l~~~g~~~~A~~~~~k  102 (723)
T 4gyw_A           26 EEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR---ISPTFADAYSNMGNTLKEMQDVQGALQCYTR  102 (723)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            6788888855   334678999999999999999999999999866   356 577999999999999999999999999


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .. +  +.| +...|+.+..+|.+.                .| +...|..+...+...|++++|.+.++++.+
T Consensus       103 Al-~--l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          103 AI-Q--INPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HH-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             HH-H--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence            88 3  455 478889998888877                44 567999999999999999999999887665

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.57  E-value=8.2e-08  Score=71.97  Aligned_cols=119  Identities=10%  Similarity=-0.018  Sum_probs=72.3

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|..+...+.+.|++++|...|++... ..  |+...+..+...+...|+++.|...++... ... +.+...|..+.
T Consensus       237 ~~~~~~~~~~~~~~~~~~~A~~~~~~~l~-~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~-~~~-~~~~~~~~~l~  311 (514)
T 2gw1_A          237 AISLEHTGIFKFLKNDPLGAHEDIKKAIE-LF--PRVNSYIYMALIMADRNDSTEYYNYFDKAL-KLD-SNNSSVYYHRG  311 (514)
T ss_dssp             HHHHHHHHHHHHHSSCHHHHHHHHHHHHH-HC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHH-TTC-TTCTHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHh-hC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHh-hcC-cCCHHHHHHHH
Confidence            45677777777777777777777777655 33  335666667777777777777777777666 211 22455566666


Q ss_pred             HHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           96 DLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        96 ~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      .+|.+.                 +.+...|..+...|...|++++|...++++.+..|+++
T Consensus       312 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  372 (514)
T 2gw1_A          312 QMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAP  372 (514)
T ss_dssp             HHHHHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCS
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCH
Confidence            555554                 22344555555666666666666666665555555443

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.57  E-value=3.9e-07  Score=62.98  Aligned_cols=133  Identities=15%  Similarity=0.088  Sum_probs=86.9

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc--HHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN--NVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|+.... ..-.|+  ...|..+-..+...|+++.|...++
T Consensus        20 ~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~   98 (272)
T 3u4t_A           20 AEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFS-KVNATKAKSADFEYYGKILMKKGQDSLAIQQYQ   98 (272)
T ss_dssp             HHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHT-TSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-ccCchhHHHHHHHHHHHHHHHcccHHHHHHHHH
Confidence            56777777552   23556888888888899999999999888765 432222  2347888888888899999998888


Q ss_pred             HhhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           77 IMVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      ... .  ..| +...|..+...|.+.                 +.+...|..+...+...+++++|...+++..+..|++
T Consensus        99 ~a~-~--~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~  175 (272)
T 3u4t_A           99 AAV-D--RDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKADSSFVKVLELKPNI  175 (272)
T ss_dssp             HHH-H--HSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTC
T ss_pred             HHH-h--cCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            887 3  223 345566666665554                 2234455555423333446677777666666665544

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.56  E-value=6.3e-07  Score=61.95  Aligned_cols=122  Identities=8%  Similarity=-0.036  Sum_probs=97.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc--HHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN--LEHYGI   93 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~--~~~~~~   93 (145)
                      ..+-..-..+.+.|++++|...|++..+ .  .| +...+..+...+...|+++.|...++... ...-.|+  ...|..
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~-~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~-~~~~~~~~~~~~~~~   79 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEA-K--KYNSPYIYNRRAVCYYELAKYDLAQKDIETYF-SKVNATKAKSADFEY   79 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHH-T--TCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHH-TTSCTTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHH-h--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHH-hccCchhHHHHHHHH
Confidence            3455667888999999999999999876 3  34 45588888889999999999999999998 4332222  334777


Q ss_pred             HHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           94 TVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        94 li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      +...|.+.                 +.+..+|..+...|...|++++|...+++..+..|.++..+
T Consensus        80 lg~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~  145 (272)
T 3u4t_A           80 YGKILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVF  145 (272)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHH
Confidence            77777766                 44667999999999999999999999999999888766543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.54  E-value=3.1e-07  Score=58.28  Aligned_cols=115  Identities=14%  Similarity=0.036  Sum_probs=88.8

Q ss_pred             HHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhc
Q 047113            6 RIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDF   82 (145)
Q Consensus         6 ~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~   82 (145)
                      ..|+....   .+...+..+-..+.+.|++++|...|+.... .. +.+...|..+-.++.+.|+++.|...|+... . 
T Consensus         5 ~~l~~al~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~-   80 (142)
T 2xcb_A            5 GTLAMLRGLSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCM-LD-HYDARYFLGLGACRQSLGLYEQALQSYSYGA-L-   80 (142)
T ss_dssp             ----CCTTCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H-
T ss_pred             hhHHHHHcCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHH-hC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHH-h-
Confidence            34554443   2456777888899999999999999999866 33 2367788888999999999999999999998 3 


Q ss_pred             CcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           83 QLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        83 ~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                       +.|+                +...|..+-.+|...|++++|...+++..+..|+++..
T Consensus        81 -~~p~----------------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~  122 (142)
T 2xcb_A           81 -MDIN----------------EPRFPFHAAECHLQLGDLDGAESGFYSARALAAAQPAH  122 (142)
T ss_dssp             -HCTT----------------CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCGGG
T ss_pred             -cCCC----------------CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCcch
Confidence             2343                55667778888999999999999999988877766543

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.53  E-value=3.5e-06  Score=60.03  Aligned_cols=128  Identities=9%  Similarity=0.041  Sum_probs=92.2

Q ss_pred             chHHHHhccC----CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HH-HHHHHHHHhhccchHHHHHHHH
Q 047113            2 DDAERIFGGI----IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NV-TFLSILFACSYSGLIEEGIKVF   75 (145)
Q Consensus         2 ~~A~~~f~~m----~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~-~~~~ll~~~~~~~~~~~a~~~~   75 (145)
                      ++|.++|++.    .+.+...|..+...+.+.|++++|..+|++..+   +.|+ .. .|..+...+.+.|+++.|..+|
T Consensus        81 ~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  157 (308)
T 2ond_A           81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKSGRMIF  157 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---SSSSCTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---ccccCccHHHHHHHHHHHHhcCHHHHHHHH
Confidence            5678888743    233566899999999999999999999999865   4564 33 7888888889999999999999


Q ss_pred             HHhhhhcCcCccHHHHHHHHHHHh---cC---------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           76 DIMVHDFQLDLNLEHYGITVDLLA---TG---------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        76 ~~m~~~~~~~~~~~~~~~li~~~~---~~---------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      ++.. ... .++...|........   ..               +.+...|..++..+.+.|++++|+.+|++..+.
T Consensus       158 ~~a~-~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~  232 (308)
T 2ond_A          158 KKAR-EDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTS  232 (308)
T ss_dssp             HHHH-TST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHS
T ss_pred             HHHH-hcC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            9888 322 223444544333321   11               445667888888888888888888888876663

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.52  E-value=5.1e-07  Score=58.45  Aligned_cols=106  Identities=11%  Similarity=0.008  Sum_probs=87.6

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +...|..+-..+.+.|++++|+..|++... .. +-+...|..+-.++.+.|+++.|...++... .  +.|+       
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al-~--~~p~-------   77 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALS-IA-PANPIYLSNRAAAYSASGQHEKAAEDAELAT-V--VDPK-------   77 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT-------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHH-H--hCCC-------
Confidence            566899999999999999999999999876 33 2267889999999999999999999999988 3  2343       


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                               +...|..+-.+|...|++++|...+++..++.|+++..
T Consensus        78 ---------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~  115 (164)
T 3sz7_A           78 ---------YSKAWSRLGLARFDMADYKGAKEAYEKGIEAEGNGGSD  115 (164)
T ss_dssp             ---------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHSSSCCH
T ss_pred             ---------CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHH
Confidence                     55677778888888999999999999988888876653

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.52  E-value=2.4e-07  Score=68.75  Aligned_cols=134  Identities=11%  Similarity=0.079  Sum_probs=83.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCC-hHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQ-EREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~-~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|+..-   +.+...|+.+-.++.+.|+ +++|+..|++... .  .| +...|+.+-.++...|++++|...|+
T Consensus       114 ~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~-l--~P~~~~a~~~~g~~~~~~g~~~eAl~~~~  190 (382)
T 2h6f_A          114 ERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE-E--QPKNYQVWHHRRVLVEWLRDPSQELEFIA  190 (382)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHTCCTTHHHHHH
T ss_pred             HHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHH-H--CCCCHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            45566666442   2356677777777777775 7777777777655 2  34 55667777777777777777777777


Q ss_pred             HhhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHh-ccChhHH-----HHHHccCC
Q 047113           77 IMVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRI-HHNVKIG-----ELVAKDPF  132 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~-~g~~~~a-----~~~~~~~~  132 (145)
                      +.. .  +.| +...|..+..++.+.                 +.+...|+.+-.++.+ .|..++|     +..+++..
T Consensus       191 kal-~--ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al  267 (382)
T 2h6f_A          191 DIL-N--QDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMI  267 (382)
T ss_dssp             HHH-H--HCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHH
T ss_pred             HHH-H--hCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence            776 2  334 455666555555443                 3345667777777776 4554666     36666666


Q ss_pred             CCCCCCCCC
Q 047113          133 HLDPKNDAY  141 (145)
Q Consensus       133 ~~~~~~~~~  141 (145)
                      ++.|+++..
T Consensus       268 ~l~P~~~~a  276 (382)
T 2h6f_A          268 KLVPHNESA  276 (382)
T ss_dssp             HHSTTCHHH
T ss_pred             HHCCCCHHH
Confidence            666665543

>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=98.51  E-value=8.7e-07  Score=53.15  Aligned_cols=106  Identities=13%  Similarity=0.041  Sum_probs=87.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ....|..+...+...|++++|...|+.... .. +.+...+..+...+...|+++.|...++... ..  .|+       
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~-~~--~~~-------   70 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIK-LD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTV-DL--KPD-------   70 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-HH--CTT-------
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHH-HC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHH-Hh--Ccc-------
Confidence            356788899999999999999999999866 32 2367788888999999999999999999988 32  232       


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                               +...|..+..++...|++++|...+++..+..|+++..
T Consensus        71 ---------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  108 (118)
T 1elw_A           71 ---------WGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQL  108 (118)
T ss_dssp             ---------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHH
T ss_pred             ---------cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHH
Confidence                     45667778888999999999999999998888876543

>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=98.51  E-value=6.2e-07  Score=60.85  Aligned_cols=134  Identities=11%  Similarity=-0.060  Sum_probs=101.8

Q ss_pred             chHHHHhccC---CC-CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGI---ID-KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m---~~-~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.+.|+..   .+ ++...|..+-.++.+.|++++|...|+....   ..| +...|..+-..+...|+++.|...++
T Consensus        24 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~  100 (228)
T 4i17_A           24 AVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIK---KNYNLANAYIGKSAAYRDMKNNQEYIATLT  100 (228)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---TTCSHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHH---hCcchHHHHHHHHHHHHHcccHHHHHHHHH
Confidence            4677777744   23 6777777799999999999999999999765   345 56688889999999999999999999


Q ss_pred             HhhhhcCcCc-cH-------HHHHHHHHHHhcC----------------CCc---hhhHHHHHHHHHhccCh--------
Q 047113           77 IMVHDFQLDL-NL-------EHYGITVDLLATG----------------ETE---PYVWGALLGACRIHHNV--------  121 (145)
Q Consensus        77 ~m~~~~~~~~-~~-------~~~~~li~~~~~~----------------~p~---~~~~~~li~~~~~~g~~--------  121 (145)
                      ....   ..| +.       ..|..+...+.+.                .|+   ...|..+-..|...|+.        
T Consensus       101 ~al~---~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~~~a~~~  177 (228)
T 4i17_A          101 EGIK---AVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLFYNNGADVLRKATPL  177 (228)
T ss_dssp             HHHH---HSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGG
T ss_pred             HHHH---HCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9882   233 33       3455555555444                554   46788888888888888        


Q ss_pred             -------------------hHHHHHHccCCCCCCCCCCC
Q 047113          122 -------------------KIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       122 -------------------~~a~~~~~~~~~~~~~~~~~  141 (145)
                                         ++|+..+++..++.|+++..
T Consensus       178 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l~p~~~~~  216 (228)
T 4i17_A          178 ASSNKEKYASEKAKADAAFKKAVDYLGEAVTLSPNRTEI  216 (228)
T ss_dssp             TTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCHHH
Confidence                               89999999999888877543

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.51  E-value=2.4e-07  Score=68.78  Aligned_cols=122  Identities=8%  Similarity=-0.033  Sum_probs=104.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccch-HHHHHHHHHHhhhhcCcCc-cHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGL-IEEGIKVFDIMVHDFQLDL-NLEHY   91 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~~~~~~-~~~~~   91 (145)
                      +...|+.+-.++.+.|++++|+..|++...   +.| +...|+.+-.++...|+ +++|...|++.. .  +.| +...|
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~---l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al-~--l~P~~~~a~  169 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIE---LNAANYTVWHFRRVLLKSLQKDLHEEMNYITAII-E--EQPKNYQVW  169 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHH-H--HCTTCHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHH---hCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHH-H--HCCCCHHHH
Confidence            346799999999999999999999999876   346 57789999999999996 999999999998 3  445 57788


Q ss_pred             HHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           92 GITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        92 ~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      +.+..+|.+.                 +.+...|..+-.++.+.|++++|+..++++.+++|+++..|
T Consensus       170 ~~~g~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~  237 (382)
T 2h6f_A          170 HHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVW  237 (382)
T ss_dssp             HHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHH
Confidence            8877777655                 45678999999999999999999999999999999876554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.50  E-value=6e-07  Score=55.21  Aligned_cols=104  Identities=10%  Similarity=0.020  Sum_probs=86.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      +...|..+...+.+.|++++|...|++... .  .| +...+..+...+...|++++|...+++.. ..  .|       
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~-~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~-~~--~~-------   81 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIK-R--NPKDAKLYSNRAACYTKLLEFQLALKDCEECI-QL--EP-------   81 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHT-T--CTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHH-HH--CT-------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-c--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHH-Hh--CC-------
Confidence            567899999999999999999999999865 2  34 67888999999999999999999999988 32  23       


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                               .+...|..+...+...|++++|...+++..+..|.++.
T Consensus        82 ---------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~  119 (133)
T 2lni_A           82 ---------TFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKE  119 (133)
T ss_dssp             ---------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGTH
T ss_pred             ---------CchHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCchH
Confidence                     24556777788889999999999999998887775543

>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=98.49  E-value=7.3e-07  Score=70.57  Aligned_cols=135  Identities=8%  Similarity=-0.158  Sum_probs=108.1

Q ss_pred             chHHHHhccCC-----------CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHH
Q 047113            2 DDAERIFGGII-----------DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIE   69 (145)
Q Consensus         2 ~~A~~~f~~m~-----------~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~   69 (145)
                      ++|.+.|++..           +.+...|..+-.++.+.|++++|...|++..+ .  .| +...|..+-.++.+.|+++
T Consensus       408 ~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~-~--~p~~~~a~~~lg~~~~~~g~~~  484 (681)
T 2pzi_A          408 VQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAE-R--VGWRWRLVWYRAVAELLTGDYD  484 (681)
T ss_dssp             HHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHH-H--HCCCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhc-c--CcchHHHHHHHHHHHHHcCCHH
Confidence            45666666543           34667899999999999999999999999876 3  34 6778898999999999999


Q ss_pred             HHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           70 EGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        70 ~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      +|...|++.. +  +.| +...|..+..+|.+.                +.+...|..+-.++.+.|++++|...+++..
T Consensus       485 ~A~~~~~~al-~--l~P~~~~~~~~lg~~~~~~g~~~~~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al  561 (681)
T 2pzi_A          485 SATKHFTEVL-D--TFPGELAPKLALAATAELAGNTDEHKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVP  561 (681)
T ss_dssp             HHHHHHHHHH-H--HSTTCSHHHHHHHHHHHHHTCCCTTCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSC
T ss_pred             HHHHHHHHHH-H--hCCCChHHHHHHHHHHHHcCChHHHHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHHhhc
Confidence            9999999988 3  345 466677776665533                4456789999999999999999999999999


Q ss_pred             CCCCCCCCCc
Q 047113          133 HLDPKNDAYY  142 (145)
Q Consensus       133 ~~~~~~~~~~  142 (145)
                      +..|+++..+
T Consensus       562 ~l~P~~~~a~  571 (681)
T 2pzi_A          562 PTSRHFTTAR  571 (681)
T ss_dssp             TTSTTHHHHH
T ss_pred             ccCcccHHHH
Confidence            9998765443

>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=98.48  E-value=1.2e-06  Score=57.23  Aligned_cols=118  Identities=10%  Similarity=0.033  Sum_probs=91.7

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHH-hhccchH--HHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFA-CSYSGLI--EEGIKVF   75 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~-~~~~~~~--~~a~~~~   75 (145)
                      ++|.+.|+..   .+.+...|..+-..+...|++++|...|+.... .. +.+...+..+..+ +...|++  +.|...+
T Consensus        27 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~la~~l~~~~~~~~~~~A~~~~  104 (177)
T 2e2e_A           27 EAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQ-LR-GENAELYAALATVLYYQASQHMTAQTRAMI  104 (177)
T ss_dssp             CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HH-CSCHHHHHHHHHHHHHHTTTCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-cC-CCCHHHHHHHHHHHHHhcCCcchHHHHHHH
Confidence            4556666643   234678899999999999999999999999866 32 2356677777777 7788998  9999999


Q ss_pred             HHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           76 DIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        76 ~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      +... ..  .|+                +...|..+...|...|++++|...+++..+..|+++.
T Consensus       105 ~~al-~~--~p~----------------~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~  150 (177)
T 2e2e_A          105 DKAL-AL--DSN----------------EITALMLLASDAFMQANYAQAIELWQKVMDLNSPRIN  150 (177)
T ss_dssp             HHHH-HH--CTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTSC
T ss_pred             HHHH-Hh--CCC----------------cHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCcc
Confidence            9888 32  332                4556777788899999999999999999988887654

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.47  E-value=7.5e-07  Score=55.87  Aligned_cols=105  Identities=12%  Similarity=-0.061  Sum_probs=86.9

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLE   89 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~   89 (145)
                      .+...|..+...+.+.|++++|...|++...   ..|+    ...+..+-.++...|+++.|...++... ..  .|+  
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~-~~--~~~--   97 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALG---LDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAI-EK--DGG--   97 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHT---SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--TSC--
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH---HcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHH-hh--Ccc--
Confidence            3567899999999999999999999999865   4566    6788888899999999999999999988 32  332  


Q ss_pred             HHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           90 HYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        90 ~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                                    +...|..+..++...|++++|...+++..+..|+++.
T Consensus        98 --------------~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~  134 (148)
T 2dba_A           98 --------------DVKALYRRSQALEKLGRLDQAVLDLQRCVSLEPKNKV  134 (148)
T ss_dssp             --------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSSCHH
T ss_pred             --------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHH
Confidence                          4556677788889999999999999998888876543

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.44  E-value=7.6e-06  Score=62.46  Aligned_cols=131  Identities=8%  Similarity=0.049  Sum_probs=99.8

Q ss_pred             hHHHHhccCC----CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-H-HHHHHHHHHhhccchHHHHHHHHH
Q 047113            3 DAERIFGGII----DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-N-VTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m~----~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~-~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      +|.++|++.-    +.+...|..+...+.+.|++++|..+|+....   +.|+ . ..|........+.|+++.|..+|+
T Consensus       304 ~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~  380 (530)
T 2ooe_A          304 EAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  380 (530)
T ss_dssp             HHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhC---ccccCchHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            6888888543    23577899999999999999999999999876   4564 2 588999988999999999999999


Q ss_pred             HhhhhcCcCc-cHHHHH--HHHHHHhcC----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           77 IMVHDFQLDL-NLEHYG--ITVDLLATG----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~--~li~~~~~~----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      +.. ..  .| +...|.  +++......                +.+...|..++..+.+.|+.++|+.+|++.....|.
T Consensus       381 ~Al-~~--~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~  457 (530)
T 2ooe_A          381 KAR-ED--ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  457 (530)
T ss_dssp             HHH-TC--TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCS
T ss_pred             HHH-hc--cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCC
Confidence            998 32  22 233332  233211111                446789999999999999999999999998776654


Q ss_pred             CC
Q 047113          138 ND  139 (145)
Q Consensus       138 ~~  139 (145)
                      +|
T Consensus       458 ~~  459 (530)
T 2ooe_A          458 PP  459 (530)
T ss_dssp             CG
T ss_pred             CH
Confidence            44

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.44  E-value=2.5e-06  Score=58.67  Aligned_cols=132  Identities=8%  Similarity=-0.022  Sum_probs=99.5

Q ss_pred             chHHHHhccCCCC----chhhHHHHHHHHHHcCChHHHHHHHHHhHhhc-----CCCC-cHHHHHHHHHHhhccchHHHH
Q 047113            2 DDAERIFGGIIDK----NVVIWSGMIASHAIHGQEREALEAFYLVIHCS-----DGKP-NNVTFLSILFACSYSGLIEEG   71 (145)
Q Consensus         2 ~~A~~~f~~m~~~----~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~-----~~~p-~~~~~~~ll~~~~~~~~~~~a   71 (145)
                      ++|.++++....+    ...+|..+...+...|++++|...|++.....     +-.| ...++..+-..+...|+++.|
T Consensus        25 ~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  104 (283)
T 3edt_B           25 KQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEA  104 (283)
T ss_dssp             HHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHH
Confidence            3455555554322    35689999999999999999999999976511     3334 466889999999999999999


Q ss_pred             HHHHHHhhhhc-----CcCc-cHHHHHHHHHHHhcC------------------------CC-chhhHHHHHHHHHhccC
Q 047113           72 IKVFDIMVHDF-----QLDL-NLEHYGITVDLLATG------------------------ET-EPYVWGALLGACRIHHN  120 (145)
Q Consensus        72 ~~~~~~m~~~~-----~~~~-~~~~~~~li~~~~~~------------------------~p-~~~~~~~li~~~~~~g~  120 (145)
                      ...+++.....     .-.| ....+..+...|...                        .| ...++..+...|...|+
T Consensus       105 ~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~  184 (283)
T 3edt_B          105 EPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGK  184 (283)
T ss_dssp             HHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCC
Confidence            99999887321     1123 467777888887766                        11 23578889999999999


Q ss_pred             hhHHHHHHccCCC
Q 047113          121 VKIGELVAKDPFH  133 (145)
Q Consensus       121 ~~~a~~~~~~~~~  133 (145)
                      +++|...+++..+
T Consensus       185 ~~~A~~~~~~~l~  197 (283)
T 3edt_B          185 YQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998765

>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=98.43  E-value=1.6e-06  Score=53.85  Aligned_cols=104  Identities=9%  Similarity=-0.083  Sum_probs=86.3

Q ss_pred             CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           13 DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        13 ~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      +.+...|..+-..+.+.|++++|...|..... .. +.+...|..+-.++...|+++.|...++... .  +.|+     
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al-~--~~p~-----   75 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAIT-RN-PLVAVYYTNRALCYLKMQQPEQALADCRRAL-E--LDGQ-----   75 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT-----
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHh-hC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHH-H--hCch-----
Confidence            34678899999999999999999999999766 33 2357789999999999999999999999988 3  2332     


Q ss_pred             HHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           93 ITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        93 ~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                                 +...|..+-..|...|++++|...+++..+..|+
T Consensus        76 -----------~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~  109 (137)
T 3q49_B           76 -----------SVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKE  109 (137)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             -----------hHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHChh
Confidence                       5567777888899999999999999988876664

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.42  E-value=2e-06  Score=53.29  Aligned_cols=102  Identities=17%  Similarity=0.002  Sum_probs=81.3

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ...+-.+-..+.+.|++++|...|+.... .  .| +...|..+-.++.+.|+++.|...|++.. .  +.|+       
T Consensus        17 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~-~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al-~--l~P~-------   83 (121)
T 1hxi_A           17 HENPMEEGLSMLKLANLAEAALAFEAVCQ-K--EPEREEAWRSLGLTQAENEKDGLAIIALNHAR-M--LDPK-------   83 (121)
T ss_dssp             CSCHHHHHHHHHHTTCHHHHHHHHHHHHH-H--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT-------
T ss_pred             chhHHHHHHHHHHcCCHHHHHHHHHHHHH-H--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCCC-------
Confidence            34577788889999999999999999876 3  45 67788889999999999999999999988 2  3443       


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                               +...|..+-.++...|++++|...+++..+..|+.+
T Consensus        84 ---------~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~  119 (121)
T 1hxi_A           84 ---------DIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYE  119 (121)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------
T ss_pred             ---------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCC
Confidence                     556777788899999999999999999988888654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.42  E-value=5.1e-07  Score=68.50  Aligned_cols=134  Identities=9%  Similarity=-0.087  Sum_probs=108.3

Q ss_pred             hHHHHhccCCC---CchhhHHHHHHHHHHcCCh-HHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            3 DAERIFGGIID---KNVVIWSGMIASHAIHGQE-REALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         3 ~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~-~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      +|.+.+++...   .+...|..+-.++.+.|++ ++|...|++..+ .  .| +...|..+-.++.+.|++++|...|+.
T Consensus        86 ~al~~l~~~~~~~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~-~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~  162 (474)
T 4abn_A           86 KTLQQMEEVLGSAQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVK-L--EPELVEAWNQLGEVYWKKGDVTSAHTCFSG  162 (474)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCchhHHHHHHHHHHHHhccccHHHHHHHHHHHHh-h--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            44555554432   3677899999999999999 999999999876 3  35 578999999999999999999999999


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC--------------------------CCchhhHHHHHHHHHhc--------cChhH
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG--------------------------ETEPYVWGALLGACRIH--------HNVKI  123 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~--------------------------~p~~~~~~~li~~~~~~--------g~~~~  123 (145)
                      .. .  +.|+...+..+..+|.+.                          +.+...|..+-.+|...        |++++
T Consensus       163 al-~--~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~  239 (474)
T 4abn_A          163 AL-T--HCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQ  239 (474)
T ss_dssp             HH-T--TCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HH-h--hCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHH
Confidence            98 3  457777788777777652                          44678899999999998        99999


Q ss_pred             HHHHHccCCCCCC---CCCCCc
Q 047113          124 GELVAKDPFHLDP---KNDAYY  142 (145)
Q Consensus       124 a~~~~~~~~~~~~---~~~~~~  142 (145)
                      |...+++..+..|   +++..+
T Consensus       240 A~~~~~~al~~~p~~~~~~~~~  261 (474)
T 4abn_A          240 ALSAYAQAEKVDRKASSNPDLH  261 (474)
T ss_dssp             HHHHHHHHHHHCGGGGGCHHHH
T ss_pred             HHHHHHHHHHhCCCcccCHHHH
Confidence            9999999888887   555443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.41  E-value=1.4e-06  Score=53.08  Aligned_cols=105  Identities=15%  Similarity=0.050  Sum_probs=85.6

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +...|..+...+...|++++|...|+.... .. +.+...+..+...+...|+++.|...++... ..  .|+       
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~-~~--~~~-------   78 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIE-LN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAI-CI--DPA-------   78 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CTT-------
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHH-cC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHH-hc--Ccc-------
Confidence            566889999999999999999999999876 32 3367788899999999999999999999988 32  332       


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                               +...|..+...+...|++++|...+++..+..|+++.
T Consensus        79 ---------~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~  115 (131)
T 2vyi_A           79 ---------YSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNET  115 (131)
T ss_dssp             ---------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHH
T ss_pred             ---------CHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCccchH
Confidence                     4556677778888999999999999988887776543

>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=98.40  E-value=5.5e-07  Score=55.59  Aligned_cols=99  Identities=10%  Similarity=-0.124  Sum_probs=83.0

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|..+-..+.+.|++++|...|.+... .. +.+...|..+-.++.+.|+++.|...++... .  +.|+        
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al-~--~~p~--------   70 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIK-RA-PEDARGYSNRAAALAKLMSFPEAIADCNKAI-E--KDPN--------   70 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT--------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHH-hC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHH-H--hCCC--------
Confidence            45688888999999999999999999866 32 2367889999999999999999999999988 3  2332        


Q ss_pred             HHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           96 DLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        96 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                              +...|..+-.++...|++++|...+++..+..
T Consensus        71 --------~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           71 --------FVRAYIRKATAQIAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             --------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             --------cHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhC
Confidence                    55677778888999999999999999988776

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.37  E-value=2.6e-06  Score=63.48  Aligned_cols=136  Identities=12%  Similarity=-0.012  Sum_probs=78.3

Q ss_pred             hHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH--HHHHHH-HHhhccchHHHHHHHHH
Q 047113            3 DAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV--TFLSIL-FACSYSGLIEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~--~~~~ll-~~~~~~~~~~~a~~~~~   76 (145)
                      +|...|+..   .+.+..+|..+-..+.+.|++++|...|++... ....|...  .+..+. -...+.|+++.|...|.
T Consensus       318 ~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~  396 (472)
T 4g1t_A          318 HAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFS-KELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFI  396 (472)
T ss_dssp             HHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHh-cCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            455555543   234667899999999999999999999999876 44443321  122222 12357889999999999


Q ss_pred             HhhhhcCcCccHHHHHHHH----HHHhcC----CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           77 IMVHDFQLDLNLEHYGITV----DLLATG----ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li----~~~~~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      +.. .  +.|+...+...+    ..+.+.    +.+..+|+.+-.+|...|++++|.+.|++..+..|..|..+
T Consensus       397 kal-~--i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~  467 (472)
T 4g1t_A          397 EGV-K--INQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSAS  467 (472)
T ss_dssp             HHH-H--SCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC--------------------
T ss_pred             HHH-h--cCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHh
Confidence            887 2  445433333222    222222    66778999999999999999999999999999877666554

>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=98.35  E-value=2e-07  Score=67.69  Aligned_cols=111  Identities=9%  Similarity=-0.040  Sum_probs=79.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----------------HHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----------------NVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----------------~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      +...|..+-..+.+.|++++|...|++... .  .|+                ...|..+-.++.+.|++++|...+++.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~-~--~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~a  222 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVS-W--LEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKA  222 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-H--TTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-H--hhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            456899999999999999999999999766 3  343                478999999999999999999999999


Q ss_pred             hhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHH-HHHHccC
Q 047113           79 VHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIG-ELVAKDP  131 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a-~~~~~~~  131 (145)
                      . .  +.| +...|..+..+|.+.                 +.+...+..+-..+.+.|+.++| ...++.|
T Consensus       223 l-~--~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  291 (336)
T 1p5q_A          223 L-E--LDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANM  291 (336)
T ss_dssp             H-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             H-H--hCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8 3  344 455555555555444                 22344555555555556666555 3344433

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.31  E-value=1.8e-05  Score=56.38  Aligned_cols=134  Identities=10%  Similarity=0.068  Sum_probs=100.2

Q ss_pred             chHHHHhccCCC--C-chh-hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHh-hccchHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K-NVV-IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFAC-SYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~~-~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~-~~~~~~~~a~~~~~   76 (145)
                      ++|.++|++.-.  | +.. .|..+...+.+.|++++|..+|++..+ .. +++...|....... ...|+++.|..+|+
T Consensus       116 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~-~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~  193 (308)
T 2ond_A          116 EKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE-DA-RTRHHVYVTAALMEYYCSKDKSVAFKIFE  193 (308)
T ss_dssp             HHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT-ST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            578888886532  3 444 899999999999999999999999876 33 23444454333332 23699999999999


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcC-------------------CC--chhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATG-------------------ET--EPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~-------------------~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      .....  ..-+...|..++..+.+.                   .|  ....|..++....+.|+.+.|..+++++.+..
T Consensus       194 ~al~~--~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~~  271 (308)
T 2ond_A          194 LGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF  271 (308)
T ss_dssp             HHHHH--HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHT
T ss_pred             HHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc
Confidence            98832  123578888888887765                   22  24588999999999999999999999998888


Q ss_pred             CCCC
Q 047113          136 PKND  139 (145)
Q Consensus       136 ~~~~  139 (145)
                      |+++
T Consensus       272 p~~~  275 (308)
T 2ond_A          272 REEY  275 (308)
T ss_dssp             TTTT
T ss_pred             cccc
Confidence            8654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.31  E-value=1.1e-06  Score=59.22  Aligned_cols=99  Identities=11%  Similarity=0.032  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHH----------------HHHHhhccchHHHHHHHHHHhhhh
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLS----------------ILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~----------------ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      +-.....+.+.|++++|...|++...   ..|+ ...|..                +-.++.+.|++++|...|+... .
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~   82 (208)
T 3urz_A            7 MLQKVSAAIEAGQNGQAVSYFRQTIA---LNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELL-Q   82 (208)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---HCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H
Confidence            33445667799999999999999865   3464 456666                8888999999999999999988 3


Q ss_pred             cCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           82 FQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        82 ~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                        +.|+                +...|..+-..+...|++++|...|++..+++|+++
T Consensus        83 --~~p~----------------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~  122 (208)
T 3urz_A           83 --KAPN----------------NVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNL  122 (208)
T ss_dssp             --HCTT----------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCH
T ss_pred             --HCCC----------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCH
Confidence              3443                334444445555555555555555555555555444

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.28  E-value=7.5e-06  Score=57.99  Aligned_cols=125  Identities=9%  Similarity=-0.047  Sum_probs=93.3

Q ss_pred             hccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc
Q 047113            8 FGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL   86 (145)
Q Consensus         8 f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~   86 (145)
                      ++...+.+...+-.+-..+.+.|++++|...|++...   ..| +...+..+...+.+.|++++|...++... .  ..|
T Consensus       109 l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~-~--~~p  182 (287)
T 3qou_A          109 LDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQ---LSNQNGEIGLLLAETLIALNRSEDAEAVLXTIP-L--QDQ  182 (287)
T ss_dssp             HHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSC-G--GGC
T ss_pred             HHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHH---hCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCc-h--hhc
Confidence            3333344556677888889999999999999999865   345 57788889999999999999999999987 2  244


Q ss_pred             cHHHHHHHHHH-Hhc-------------C----CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           87 NLEHYGITVDL-LAT-------------G----ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        87 ~~~~~~~li~~-~~~-------------~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      +.......... +.+             .    +.+...+..+-..+...|++++|...+.++.+..|+.
T Consensus       183 ~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~  252 (287)
T 3qou_A          183 DTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTA  252 (287)
T ss_dssp             SHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTG
T ss_pred             chHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccc
Confidence            43322222111 111             1    4466789999999999999999999999999888865

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.27  E-value=7.5e-06  Score=57.98  Aligned_cols=125  Identities=8%  Similarity=-0.080  Sum_probs=88.0

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC-cHHHHHHHHHHhhcc-chHHHHHHHHHHhhhhc---CcCcc
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP-NNVTFLSILFACSYS-GLIEEGIKVFDIMVHDF---QLDLN   87 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p-~~~~~~~ll~~~~~~-~~~~~a~~~~~~m~~~~---~~~~~   87 (145)
                      ..+|+.+-.+|.+.|++++|+..|+.....   .|-.+ -..+++.+-..+... |++++|...|++.....   +-.+.
T Consensus        77 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~  156 (292)
T 1qqe_A           77 GNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVAL  156 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHH
Confidence            468999999999999999999999886441   11111 145788888899996 99999999999887311   11111


Q ss_pred             -HHHHHHHHHHHhcC----------------CCch--------hhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           88 -LEHYGITVDLLATG----------------ETEP--------YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        88 -~~~~~~li~~~~~~----------------~p~~--------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                       ..++..+...|.+.                .|+.        ..|..+..++...|++++|...+++..++.|+.+.
T Consensus       157 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~  234 (292)
T 1qqe_A          157 SNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFAD  234 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC------
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCC
Confidence             35677777777766                2321        15677788899999999999999999998886543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.26  E-value=1.2e-06  Score=61.29  Aligned_cols=121  Identities=7%  Similarity=-0.003  Sum_probs=85.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhc------CCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc-----
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCS------DGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF-----   82 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~------~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-----   82 (145)
                      ....|..+...+.+.|++++|...|++... .      +-.| ...++..+...+...|++++|...+++.....     
T Consensus       152 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  230 (311)
T 3nf1_A          152 VAKQLNNLALLCQNQGKYEEVEYYYQRALE-IYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREF  230 (311)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHH-HHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcC
Confidence            345799999999999999999999999866 3      2244 35578899999999999999999999988311     


Q ss_pred             -CcCccHHHHHHHHHHHhcC-----------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           83 -QLDLNLEHYGITVDLLATG-----------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        83 -~~~~~~~~~~~li~~~~~~-----------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                       ...+...........+...                       .| +..+|..+...|.+.|++++|...+++..++.|
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~~  309 (311)
T 3nf1_A          231 GSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRK  309 (311)
T ss_dssp             C------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC
T ss_pred             CCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence             1122111111111111111                       23 446889999999999999999999998766544

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.26  E-value=7e-06  Score=59.25  Aligned_cols=127  Identities=11%  Similarity=-0.022  Sum_probs=93.5

Q ss_pred             HHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCC-CcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113            4 AERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGK-PNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus         4 A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      |.+.|++.-   +++..++..+-.++...|++++|++++.+-.. .+-. -+...+..++..+.+.|+.+.|...++.|.
T Consensus        85 a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~-~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGID-NDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT-SSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhc-cCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            445566443   24555667888999999999999999998644 3321 267788999999999999999999999998


Q ss_pred             hhcCcCc-----cHHHHHHHHHHHhcC--------------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           80 HDFQLDL-----NLEHYGITVDLLATG--------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        80 ~~~~~~~-----~~~~~~~li~~~~~~--------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                       +  ..|     +-.+...|..++...                    .|++.+-..++.++.+.|++++|.+.++.+.+.
T Consensus       164 -~--~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~  240 (310)
T 3mv2_B          164 -N--AIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSD  240 (310)
T ss_dssp             -H--HSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSH
T ss_pred             -h--cCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             3  355     244444444443321                    666556667777899999999999999876664

>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=98.26  E-value=4.1e-06  Score=52.21  Aligned_cols=105  Identities=8%  Similarity=-0.011  Sum_probs=81.5

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGI   93 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~   93 (145)
                      ...|..|-..+.+.|++++|+..|++..+ .  .| +...|+.+-.++.+.|+++.|...++... .  +.|+ ...|..
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~-~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al-~--~~~~~~~~~~~   81 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIE-L--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAV-E--VGRETRADYKL   81 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHH-H--hCcccchhhHH
Confidence            34688999999999999999999999876 3  45 67789999999999999999999999887 2  2222 111211


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      +          ..+|..+-.++...|++++|.+.|++..+..|
T Consensus        82 ~----------a~~~~~lg~~~~~~~~~~~A~~~~~kal~~~~  114 (127)
T 4gcn_A           82 I----------AKAMSRAGNAFQKQNDLSLAVQWFHRSLSEFR  114 (127)
T ss_dssp             H----------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSC
T ss_pred             H----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc
Confidence            1          13456677888999999999999998766555

>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=98.23  E-value=1.5e-06  Score=57.90  Aligned_cols=106  Identities=10%  Similarity=-0.073  Sum_probs=74.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc--------------HHHHHHHHHHhhccchHHHHHHHHHHhhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN--------------NVTFLSILFACSYSGLIEEGIKVFDIMVH   80 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~--------------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~   80 (145)
                      ....|..+-..+.+.|++++|...|++......-.|+              ...|..+-.++.+.|+++.|...++... 
T Consensus        37 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al-  115 (198)
T 2fbn_A           37 SAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVL-  115 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH-
Confidence            3456888889999999999999999997651111221              2678888889999999999999999988 


Q ss_pred             hcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           81 DFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        81 ~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ..  .|+                +...|..+-.+|...|++++|...+++..+..|+++
T Consensus       116 ~~--~p~----------------~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~  156 (198)
T 2fbn_A          116 KI--DKN----------------NVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNL  156 (198)
T ss_dssp             HH--STT----------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCH
T ss_pred             Hh--Ccc----------------cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcH
Confidence            32  332                334455555666666666666666666655555443

>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=98.20  E-value=1.3e-05  Score=50.95  Aligned_cols=114  Identities=4%  Similarity=-0.117  Sum_probs=76.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|..+-..+.+.|++++|...|..... .. +.+...+..+...+...|+++.|...++... ... ..+...|..+.
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~-~~~-~~~~~~~~~~a   88 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIE-LN-PSNAIYYGNRSLAYLRTECYGYALGDATRAI-ELD-KKYIKGYYRRA   88 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHH-hC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhC-cccHHHHHHHH
Confidence            34677788888888888888888888765 32 2256777788888888888888888888877 321 22455666666


Q ss_pred             HHHhcC-----------------CCchhhHHHHH--HHHHhccChhHHHHHHccCCC
Q 047113           96 DLLATG-----------------ETEPYVWGALL--GACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        96 ~~~~~~-----------------~p~~~~~~~li--~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .+|.+.                 +.+...+..+-  ..+.+.|++++|...++....
T Consensus        89 ~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           89 ASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            555554                 22444453333  336677888888888776554

>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=98.19  E-value=4.3e-05  Score=46.33  Aligned_cols=96  Identities=14%  Similarity=0.175  Sum_probs=77.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.++|+.+.   +.+...|..+...+.+.|++++|...|+++.. .+ +.+...+..+...+.+.|+++.|...++.+
T Consensus        18 ~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~   95 (136)
T 2fo7_A           18 DEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE-LD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKA   95 (136)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHH-HC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            56778887653   34677899999999999999999999999876 43 346778889999999999999999999999


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                      . ... ..+...+..+..+|.+.
T Consensus        96 ~-~~~-~~~~~~~~~la~~~~~~  116 (136)
T 2fo7_A           96 L-ELD-PRSAEAWYNLGNAYYKQ  116 (136)
T ss_dssp             H-HHC-TTCHHHHHHHHHHHHTT
T ss_pred             H-HhC-CCChHHHHHHHHHHHHH
Confidence            8 322 33577788888888766

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.18  E-value=7.4e-05  Score=51.80  Aligned_cols=60  Identities=3%  Similarity=-0.181  Sum_probs=28.8

Q ss_pred             hhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHHHHHHHhh
Q 047113           16 VVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGIKVFDIMV   79 (145)
Q Consensus        16 ~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~   79 (145)
                      ...+..+-..+.+    .+++++|...|++..+ .+   +...+..+-..+..    .+++++|...|++..
T Consensus        38 ~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~-~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~  105 (273)
T 1ouv_A           38 NSGCFNLGVLYYQGQGVEKNLKKAASFYAKACD-LN---YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKAC  105 (273)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHH
Confidence            3444444455555    5555555555555444 22   34444444444444    555555555555444

>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=98.18  E-value=1.3e-05  Score=56.63  Aligned_cols=103  Identities=10%  Similarity=-0.053  Sum_probs=85.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      +...|..+-..+.+.|++++|...|+.... .  .| +...|..+-.++.+.|++++|...++... .  +.|+      
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~-~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al-~--~~p~------   70 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAIT-R--NPLVAVYYTNRALCYLKMQQPEQALADCRRAL-E--LDGQ------   70 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHT-T--SCTT------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHH-H--hCCC------
Confidence            456788889999999999999999999866 3  45 67888999999999999999999999988 3  3443      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                                +...+..+-.+|...|++++|...+++..+..|+++
T Consensus        71 ----------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~  106 (281)
T 2c2l_A           71 ----------SVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQR  106 (281)
T ss_dssp             ----------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             ----------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccch
Confidence                      556777788888999999999999998887776554

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.17  E-value=8.6e-06  Score=55.97  Aligned_cols=28  Identities=7%  Similarity=-0.024  Sum_probs=24.2

Q ss_pred             hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113          106 YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus       106 ~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .++..+...|...|++++|...+++..+
T Consensus       253 ~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          253 TTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4788889999999999999999987554

>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=98.17  E-value=1.6e-05  Score=48.36  Aligned_cols=103  Identities=6%  Similarity=-0.075  Sum_probs=82.1

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ..+|..+...+.+.|++++|...|.+... .. +.+...+..+...+...|+++.|...++... ...  |+.       
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~-~~~--~~~-------   71 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKE-LD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAI-EVG--REN-------   71 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-HHH--HHS-------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHh-cC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHH-hhc--ccc-------
Confidence            45788899999999999999999999876 33 3467788899999999999999999999988 321  110       


Q ss_pred             HHHhcCCCc----hhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           96 DLLATGETE----PYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        96 ~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                            .++    ..+|..+...+...|++++|...+++..+..|
T Consensus        72 ------~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~  110 (131)
T 1elr_A           72 ------REDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHR  110 (131)
T ss_dssp             ------TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC
T ss_pred             ------chhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC
Confidence                  011    45667778889999999999999998877666

>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=98.16  E-value=1.1e-05  Score=53.84  Aligned_cols=100  Identities=14%  Similarity=-0.007  Sum_probs=83.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...+..+-..+.+.|++++|...|++.     +.|+...+..+-..+.+.|+++.|...++... ..  .|         
T Consensus         6 ~~~~~~~g~~~~~~~~~~~A~~~~~~a-----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~~--~~---------   68 (213)
T 1hh8_A            6 AISLWNEGVLAADKKDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSI-NR--DK---------   68 (213)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CT---------
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHH-----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHH-Hh--Cc---------
Confidence            345667788889999999999999865     35688899999999999999999999999988 32  23         


Q ss_pred             HHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           96 DLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        96 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                             .+...|..+-..|...|++++|...+++..+..|.++
T Consensus        69 -------~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~  105 (213)
T 1hh8_A           69 -------HLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQ  105 (213)
T ss_dssp             -------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCS
T ss_pred             -------cchHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcc
Confidence                   2556778888999999999999999999888777554

>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=98.16  E-value=1.7e-05  Score=51.82  Aligned_cols=113  Identities=7%  Similarity=-0.067  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      +-.+...+.+.|++++|...|++..+   ..| +...+..+-..+.+.|++++|...++.....   .|+...+..+...
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~---~p~~~~~~~~~~~   82 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSD---ELQSRGDVKLAKADCLLETKQFELAQELLATIPLE---YQDNSYKSLIAKL   82 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCH---HHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG---GCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---HCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc---cCChHHHHHHHHH
Confidence            44455556666666666666666433   123 4455666666666666666666666665522   1222211111100


Q ss_pred             --------------HhcC---CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           98 --------------LATG---ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        98 --------------~~~~---~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                                    +-+.   .| +...+..+-..+...|++++|...++++.+..|+
T Consensus        83 ~~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~  140 (176)
T 2r5s_A           83 ELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLG  140 (176)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT
T ss_pred             HHHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcc
Confidence                          0000   33 4566777777777777777777777777776664

>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=98.15  E-value=2.4e-06  Score=64.53  Aligned_cols=102  Identities=12%  Similarity=0.029  Sum_probs=69.8

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----------------HHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----------------NVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----------------~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ....|..+-..+.+.|++++|...|++... .  .|+                ...|..+-.++.+.|+++.|...+++.
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~-~--~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~a  343 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVS-W--LEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKA  343 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--HTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-H--hcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            455788999999999999999999999765 2  232                578889999999999999999999999


Q ss_pred             hhhcCcCc-cHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           79 VHDFQLDL-NLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      . .  +.| +...|..                 +-.+|...|++++|...|++..++.|+++
T Consensus       344 l-~--~~p~~~~a~~~-----------------~g~a~~~~g~~~~A~~~~~~al~l~P~~~  385 (457)
T 1kt0_A          344 L-G--LDSANEKGLYR-----------------RGEAQLLMNEFESAKGDFEKVLEVNPQNK  385 (457)
T ss_dssp             H-H--HSTTCHHHHHH-----------------HHHHHHHTTCHHHHHHHHHHHHTTC----
T ss_pred             H-h--cCCccHHHHHH-----------------HHHHHHHccCHHHHHHHHHHHHHhCCCCH
Confidence            8 3  334 3444444                 44444444555555555554444444433

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.15  E-value=6.8e-05  Score=51.97  Aligned_cols=126  Identities=10%  Similarity=-0.060  Sum_probs=79.0

Q ss_pred             chHHHHhccCCC-CchhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHH
Q 047113            2 DDAERIFGGIID-KNVVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m~~-~~~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~   72 (145)
                      ++|.+.|+...+ .+...|..+-..|.+    .+++++|...|+...+ .+   +...+..+-..+..    .+++++|.
T Consensus        59 ~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~-~~---~~~a~~~lg~~~~~~~~~~~~~~~A~  134 (273)
T 1ouv_A           59 KKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACD-LK---YAEGCASLGGIYHDGKVVTRDFKKAV  134 (273)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHH-cC---CccHHHHHHHHHHcCCCcccCHHHHH
Confidence            345555554422 356667777777777    7777777777777666 43   56666666666766    77777777


Q ss_pred             HHHHHhhhhcCcCccHHHHHHHHHHHhc----C---------------CCchhhHHHHHHHHHh----ccChhHHHHHHc
Q 047113           73 KVFDIMVHDFQLDLNLEHYGITVDLLAT----G---------------ETEPYVWGALLGACRI----HHNVKIGELVAK  129 (145)
Q Consensus        73 ~~~~~m~~~~~~~~~~~~~~~li~~~~~----~---------------~p~~~~~~~li~~~~~----~g~~~~a~~~~~  129 (145)
                      ..|++.. +.+   +...+..+...|.+    .               ..+...+..+-..|..    .+++++|...++
T Consensus       135 ~~~~~a~-~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~  210 (273)
T 1ouv_A          135 EYFTKAC-DLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYS  210 (273)
T ss_dssp             HHHHHHH-HTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHH
T ss_pred             HHHHHHH-hcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHH
Confidence            7777776 433   34455555555554    2               3344556666666666    777777777776


Q ss_pred             cCCCCC
Q 047113          130 DPFHLD  135 (145)
Q Consensus       130 ~~~~~~  135 (145)
                      +..+..
T Consensus       211 ~a~~~~  216 (273)
T 1ouv_A          211 KACELE  216 (273)
T ss_dssp             HHHHTT
T ss_pred             HHHhCC
Confidence            655443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.10  E-value=7.4e-05  Score=51.58  Aligned_cols=135  Identities=9%  Similarity=-0.025  Sum_probs=86.0

Q ss_pred             chHHHHhccCCC--C-c---hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhc--------cc
Q 047113            2 DDAERIFGGIID--K-N---VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSY--------SG   66 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~---~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~--------~~   66 (145)
                      ++|.+.|+.+..  | +   ...|..+-.++.+.|++++|...|+.......-.|. ...+..+-.++..        .|
T Consensus        32 ~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~  111 (261)
T 3qky_A           32 DRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQT  111 (261)
T ss_dssp             HHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCH
T ss_pred             HHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccch
Confidence            567777776632  3 3   456778888888888888888888887651211222 3455566666666        88


Q ss_pred             hHHHHHHHHHHhhhhcCcCcc-HHHH-----------------HHHHHHHhcC----------------CCc----hhhH
Q 047113           67 LIEEGIKVFDIMVHDFQLDLN-LEHY-----------------GITVDLLATG----------------ETE----PYVW  108 (145)
Q Consensus        67 ~~~~a~~~~~~m~~~~~~~~~-~~~~-----------------~~li~~~~~~----------------~p~----~~~~  108 (145)
                      +++.|...|+.....   .|+ ...+                 ..+...|.+.                .|+    ...+
T Consensus       112 ~~~~A~~~~~~~l~~---~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~  188 (261)
T 3qky_A          112 DTRKAIEAFQLFIDR---YPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDAL  188 (261)
T ss_dssp             HHHHHHHHHHHHHHH---CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHH
T ss_pred             hHHHHHHHHHHHHHH---CcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHH
Confidence            888888888888732   222 2222                 2233344433                343    2356


Q ss_pred             HHHHHHHHhc----------cChhHHHHHHccCCCCCCCCC
Q 047113          109 GALLGACRIH----------HNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       109 ~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ..+..+|...          |++++|...++++.+..|+++
T Consensus       189 ~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~  229 (261)
T 3qky_A          189 VGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDSP  229 (261)
T ss_dssp             HHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCCh
Confidence            6666777655          777888888888777777654

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.10  E-value=1.7e-05  Score=48.54  Aligned_cols=102  Identities=10%  Similarity=-0.091  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-H---HHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-N---VTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~---~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +-.+-..+.+.|++++|...|+.... ..  |+ .   ..+..+-.++.+.|+++.|...++... ..  .|+..     
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~-~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~-~~--~p~~~-----   73 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLE-LY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLV-SR--YPTHD-----   73 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH-HC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CTTST-----
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHH-HC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHH-HH--CCCCc-----
Confidence            44566778899999999999999866 32  33 3   477778888999999999999999988 32  23200     


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                              .....+..+-..+...|++++|...++++.+..|+++
T Consensus        74 --------~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~  110 (129)
T 2xev_A           74 --------KAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQYPGSD  110 (129)
T ss_dssp             --------THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTSH
T ss_pred             --------ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCh
Confidence                    0034556677888899999999999999888777654

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.10  E-value=8.3e-06  Score=52.49  Aligned_cols=104  Identities=11%  Similarity=-0.034  Sum_probs=84.0

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhc--------C--------CCC-cHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCS--------D--------GKP-NNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~--------~--------~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ...|...-..+.+.|++++|+..|..... .        .        +.| +...|..+-.++.+.|+++.|...++..
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~a   89 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALT-RLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEV   89 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            45788889999999999999999999765 3        0        022 3467888899999999999999999998


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      . .  +.|+                +...|..+-.+|...|++++|...+++..++.|+++
T Consensus        90 l-~--~~p~----------------~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~  131 (162)
T 3rkv_A           90 L-K--REET----------------NEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAA  131 (162)
T ss_dssp             H-H--HSTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGH
T ss_pred             H-h--cCCc----------------chHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCH
Confidence            8 3  3443                556777788889999999999999999888888654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.09  E-value=2.8e-05  Score=54.27  Aligned_cols=118  Identities=7%  Similarity=-0.016  Sum_probs=88.7

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhc-------CCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhc-----
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCS-------DGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDF-----   82 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~-------~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-----   82 (145)
                      +..+|..+...+...|++++|..+|+++.+ .       .-......+..+...+...|+++.|...++......     
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~-~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  104 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALE-DLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLG  104 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhC
Confidence            356788899999999999999999988765 2       222346678888888899999999999988887321     


Q ss_pred             CcCc-cHHHHHHHHHHHhcC------------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           83 QLDL-NLEHYGITVDLLATG------------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        83 ~~~~-~~~~~~~li~~~~~~------------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      +-.| ....+..+...|...                        .| ...++..+...|...|++++|...+++..+
T Consensus       105 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~  181 (311)
T 3nf1_A          105 KDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALE  181 (311)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2223 466677777777666                        12 234688888999999999999999998766

>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=98.08  E-value=2.5e-05  Score=59.42  Aligned_cols=106  Identities=7%  Similarity=-0.030  Sum_probs=76.1

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|++.   .+.+...|..+-.++.+.|++++|...|++..+ .  .| +...|..+-.++.+.|++++|...+++
T Consensus        23 ~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-l--~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~   99 (477)
T 1wao_1           23 ENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIE-L--DKKYIKGYYRRAASNMALGKFRAALRDYET   99 (477)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-S--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-h--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            4677777744   234677899999999999999999999998876 3  44 577888888899999999999999998


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHH--HHhccChhHHHHHHc
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGA--CRIHHNVKIGELVAK  129 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~--~~~~g~~~~a~~~~~  129 (145)
                      .. +  +.|+                +...+..+-.+  +.+.|++++|.+.++
T Consensus       100 al-~--~~p~----------------~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1          100 VV-K--VKPH----------------DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HH-H--HSTT----------------CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HH-H--hCCC----------------CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            87 3  2332                33344444444  788899999999999

>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=98.08  E-value=8.7e-06  Score=53.24  Aligned_cols=109  Identities=9%  Similarity=-0.065  Sum_probs=84.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-------------HHHHHHHHHHhhccchHHHHHHHHHHhhhhcC
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-------------NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ   83 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-------------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~   83 (145)
                      ..|...-..+.+.|++++|+..|+...+   +.|+             ...|+.+-.++.+.|++++|...+++.. .  
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~---l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL-~--   85 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAME---ISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL-H--   85 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH---HHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHh---hCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H--
Confidence            4577788889999999999999999765   2343             2388999999999999999999999988 3  


Q ss_pred             cCccHHHHHHHHHHHhcCCC-chhhH----HHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           84 LDLNLEHYGITVDLLATGET-EPYVW----GALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        84 ~~~~~~~~~~li~~~~~~~p-~~~~~----~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +          .+--.+..| +...|    ...-.++...|++++|+..|++..++.|.+...
T Consensus        86 l----------~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~  138 (159)
T 2hr2_A           86 Y----------FNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGE  138 (159)
T ss_dssp             H----------HHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSC
T ss_pred             h----------hhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHH
Confidence            2          000011122 44567    778899999999999999999999888866554

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.05  E-value=0.00021  Score=49.21  Aligned_cols=124  Identities=9%  Similarity=-0.075  Sum_probs=93.4

Q ss_pred             CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-c---HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-c
Q 047113           13 DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-N---NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-N   87 (145)
Q Consensus        13 ~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~---~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~   87 (145)
                      +.+...+-.+-..+.+.|++++|...|+.... .  .| +   ...+..+-.++.+.|+++.|...|+.......-.| .
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~-~--~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~   88 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFT-Y--GRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRV   88 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGG-G--CSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-h--CCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchh
Confidence            34666777888899999999999999999876 3  24 3   56788888899999999999999999984322122 2


Q ss_pred             HHHHHHHHHHHhc--------C----------------CCc-hhhH-----------------HHHHHHHHhccChhHHH
Q 047113           88 LEHYGITVDLLAT--------G----------------ETE-PYVW-----------------GALLGACRIHHNVKIGE  125 (145)
Q Consensus        88 ~~~~~~li~~~~~--------~----------------~p~-~~~~-----------------~~li~~~~~~g~~~~a~  125 (145)
                      ...+..+..+|.+        .                .|+ ...+                 -.+-..|.+.|++++|.
T Consensus        89 ~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  168 (261)
T 3qky_A           89 PQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAA  168 (261)
T ss_dssp             HHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHH
Confidence            4556666666655        3                443 3344                 44567889999999999


Q ss_pred             HHHccCCCCCCCCC
Q 047113          126 LVAKDPFHLDPKND  139 (145)
Q Consensus       126 ~~~~~~~~~~~~~~  139 (145)
                      ..++++.+..|+++
T Consensus       169 ~~~~~~l~~~p~~~  182 (261)
T 3qky_A          169 VTYEAVFDAYPDTP  182 (261)
T ss_dssp             HHHHHHHHHCTTST
T ss_pred             HHHHHHHHHCCCCc
Confidence            99999988877644

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.05  E-value=1.7e-05  Score=57.54  Aligned_cols=105  Identities=12%  Similarity=-0.026  Sum_probs=73.5

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH------------------HHHHHHHHhhccchHHHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV------------------TFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~------------------~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ...|..+-..+.+.|++++|...|++...   +.|+..                  .|+.+-.++.+.|+++.|...++.
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~---~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~  255 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIA---YMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNI  255 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHH---HSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH---HhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            45688888899999999999999999655   245443                  788888899999999999999998


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      .. .  +.|+                +...|..+-.+|...|++++|...|++..++.|+++..+
T Consensus       256 al-~--~~p~----------------~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~  301 (338)
T 2if4_A          256 VL-T--EEEK----------------NPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIR  301 (338)
T ss_dssp             HH-H--HCTT----------------CHHHHHHHHHHHHTTTCHHHHHHHHHHTTC---------
T ss_pred             HH-H--hCCC----------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHH
Confidence            88 3  2332                445556666677777777777777777777766655443

>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=98.04  E-value=6.8e-07  Score=57.42  Aligned_cols=97  Identities=6%  Similarity=-0.016  Sum_probs=77.3

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCC
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGE  102 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~  102 (145)
                      ..+...|++++|+..+.....   ..| +...+-.+-..|.+.|+++.|...|++.. .  +.|+               
T Consensus         5 ~~~~~~~~~e~ai~~~~~a~~---~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al-~--~~p~---------------   63 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGSTP---SPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYI-N--VQER---------------   63 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHHSC---SHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT---------------
T ss_pred             HHHHHcChHHHHHHHHHHhcc---cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCCC---------------
Confidence            445567889999999988643   345 34466678888999999999999999998 3  3443               


Q ss_pred             CchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113          103 TEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus       103 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                       +..+|..+-..|...|++++|...|++..+++|+++..+
T Consensus        64 -~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~  102 (150)
T 4ga2_A           64 -DPKAHRFLGLLYELEENTDKAVECYRRSVELNPTQKDLV  102 (150)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             -CHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCCCHHHH
Confidence             667888888999999999999999999999999877654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.03  E-value=0.00013  Score=43.58  Aligned_cols=92  Identities=17%  Similarity=0.204  Sum_probs=70.4

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+++.   +.+..+|..+...+.+.|++++|...|+.+.. .. +.+..++..+...+.+.|+++.|...++.+
T Consensus        26 ~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  103 (125)
T 1na0_A           26 DEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE-LD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKA  103 (125)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-hC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            46777777653   34677899999999999999999999999876 43 346778899999999999999999999998


Q ss_pred             hhhcCcCccHHHHHHHHHH
Q 047113           79 VHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~   97 (145)
                      . +.. +.+...+..+..+
T Consensus       104 ~-~~~-~~~~~~~~~l~~~  120 (125)
T 1na0_A          104 L-ELD-PNNAEAKQNLGNA  120 (125)
T ss_dssp             H-HHC-TTCHHHHHHHHHH
T ss_pred             H-HhC-CCcHHHHHHHHHH
Confidence            8 322 1234444444433

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.02  E-value=1.9e-06  Score=52.73  Aligned_cols=75  Identities=15%  Similarity=0.156  Sum_probs=50.4

Q ss_pred             chHHHHhccCCC-----C-chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID-----K-NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~-----~-~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|...|+....     | +...|..+-..+.+.|++++|...|++..+ .  .| +...+..+-.++.+.|++++|...
T Consensus         7 ~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~-~--~p~~~~~~~~l~~~~~~~g~~~~A~~~   83 (117)
T 3k9i_A            7 AQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVK-Q--FPNHQALRVFYAMVLYNLGRYEQGVEL   83 (117)
T ss_dssp             CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-h--CCCchHHHHHHHHHHHHcCCHHHHHHH
Confidence            456666664422     2 345677777777777777777777777655 2  23 456667777777777777777777


Q ss_pred             HHHhh
Q 047113           75 FDIMV   79 (145)
Q Consensus        75 ~~~m~   79 (145)
                      +++..
T Consensus        84 ~~~al   88 (117)
T 3k9i_A           84 LLKII   88 (117)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77766

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.01  E-value=3.6e-05  Score=50.64  Aligned_cols=132  Identities=10%  Similarity=-0.081  Sum_probs=90.3

Q ss_pred             chHHH---HhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHh---hcCCCC-cHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAER---IFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIH---CSDGKP-NNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~---~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~---~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.+   .+..-+.....+|+.+-..+...|++++|...|++...   +.+..| ....++.+-..+...|+++.|...
T Consensus         9 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~   88 (203)
T 3gw4_A            9 ALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRC   88 (203)
T ss_dssp             HHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            46777   55443334567899999999999999999999988543   122333 345778888889999999999999


Q ss_pred             HHHhhhh---cCcCc--cHHHHHHHHHHHhcC-------------------CCc----hhhHHHHHHHHHhccChhHHHH
Q 047113           75 FDIMVHD---FQLDL--NLEHYGITVDLLATG-------------------ETE----PYVWGALLGACRIHHNVKIGEL  126 (145)
Q Consensus        75 ~~~m~~~---~~~~~--~~~~~~~li~~~~~~-------------------~p~----~~~~~~li~~~~~~g~~~~a~~  126 (145)
                      +++....   .+-.|  ....+..+...|...                   ..+    ..++..+-..+...|++++|..
T Consensus        89 ~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  168 (203)
T 3gw4_A           89 FLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQ  168 (203)
T ss_dssp             HHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHH
Confidence            9887732   22122  233455555555544                   122    2345777888899999999998


Q ss_pred             HHccCCC
Q 047113          127 VAKDPFH  133 (145)
Q Consensus       127 ~~~~~~~  133 (145)
                      .+++..+
T Consensus       169 ~~~~al~  175 (203)
T 3gw4_A          169 HWLRARD  175 (203)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.00  E-value=9.4e-05  Score=45.90  Aligned_cols=90  Identities=12%  Similarity=0.040  Sum_probs=71.9

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|++.   .+.+...|..+-.++.+.|++++|+..|+...+ .+ +.+...|..+-.++...|++++|...|+..
T Consensus        30 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~-~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~a  107 (126)
T 4gco_A           30 PTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIR-LD-SKFIKGYIRKAACLVAMREWSKAQRAYEDA  107 (126)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHH-hh-hhhhHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            5788888854   345788999999999999999999999999876 33 236788999999999999999999999999


Q ss_pred             hhhcCcCcc-HHHHHHHHH
Q 047113           79 VHDFQLDLN-LEHYGITVD   96 (145)
Q Consensus        79 ~~~~~~~~~-~~~~~~li~   96 (145)
                      . +  +.|+ ...+..|-.
T Consensus       108 l-~--l~P~~~~a~~~l~~  123 (126)
T 4gco_A          108 L-Q--VDPSNEEAREGVRN  123 (126)
T ss_dssp             H-H--HCTTCHHHHHHHHH
T ss_pred             H-H--HCcCCHHHHHHHHH
Confidence            8 3  4563 555544443

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.99  E-value=0.00016  Score=45.84  Aligned_cols=76  Identities=13%  Similarity=0.102  Sum_probs=63.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|+.... .. +.+...+..+-.++...|+++.|...++..
T Consensus        30 ~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a  107 (166)
T 1a17_A           30 ENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIE-LD-KKYIKGYYRRAASNMALGKFRAALRDYETV  107 (166)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-cccHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            45677777542   34678899999999999999999999999876 32 336778889999999999999999999998


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       108 ~  108 (166)
T 1a17_A          108 V  108 (166)
T ss_dssp             H
T ss_pred             H
Confidence            8

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.99  E-value=4.6e-05  Score=46.36  Aligned_cols=70  Identities=14%  Similarity=-0.040  Sum_probs=51.4

Q ss_pred             HcCChHHHHHHHHHhHhhcCC-CC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC
Q 047113           28 IHGQEREALEAFYLVIHCSDG-KP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG  101 (145)
Q Consensus        28 ~~g~~~~A~~~~~~m~~~~~~-~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~  101 (145)
                      ..|++++|+..|++..+ .+. .| +...+..+-.++...|++++|...|++.. ..  .| +...+..+..+|.+.
T Consensus         2 ~~g~~~~A~~~~~~al~-~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~~--~p~~~~~~~~l~~~~~~~   74 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIA-SGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGV-KQ--FPNHQALRVFYAMVLYNL   74 (117)
T ss_dssp             -----CCCHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CTTCHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHH-cCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-Hh--CCCchHHHHHHHHHHHHc
Confidence            46899999999999876 321 24 46688899999999999999999999998 32  34 477777788777766

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=97.98  E-value=0.0001  Score=52.04  Aligned_cols=121  Identities=8%  Similarity=-0.030  Sum_probs=82.8

Q ss_pred             hhhHHHHHHHHHHc-CChHHHHHHHHHhHhh---cCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cH-
Q 047113           16 VVIWSGMIASHAIH-GQEREALEAFYLVIHC---SDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NL-   88 (145)
Q Consensus        16 ~~~~~~li~a~~~~-g~~~~A~~~~~~m~~~---~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~-   88 (145)
                      ..+|+.+-..|.+. |++++|+..|++....   .+-.+. ..+++.+-..+.+.|++++|...|+... ...... .. 
T Consensus       117 a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~~~~~~~~~~  195 (292)
T 1qqe_A          117 ANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLI-KSSMGNRLSQ  195 (292)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HTTSSCTTTG
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH-HHHhcCCccc
Confidence            35799999999996 9999999999986540   111111 3578888999999999999999999988 432221 11 


Q ss_pred             ----HHHHHHHHHHhcC----------------CCch------hhHHHHHHHHH--hccChhHHHHHHccCCCCCCC
Q 047113           89 ----EHYGITVDLLATG----------------ETEP------YVWGALLGACR--IHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        89 ----~~~~~li~~~~~~----------------~p~~------~~~~~li~~~~--~~g~~~~a~~~~~~~~~~~~~  137 (145)
                          ..|..+..+|...                .|+.      ..+..++.+|.  ..+++++|...|+.+.+++|.
T Consensus       196 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~~  272 (292)
T 1qqe_A          196 WSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKW  272 (292)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHHH
Confidence                1455555555543                3332      13455666665  467899999999998887764

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=97.93  E-value=0.00027  Score=53.84  Aligned_cols=117  Identities=10%  Similarity=0.075  Sum_probs=89.3

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      .|...|..++. +.+.|++++|..+|+++.+  ..+-+...|...+..+.+.|+++.|..+|++.. .  ..|+...|..
T Consensus        11 ~~~~~w~~l~~-~~~~~~~~~a~~~~e~al~--~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral-~--~~p~~~lw~~   84 (530)
T 2ooe_A           11 YDLDAWSILIR-EAQNQPIDKARKTYERLVA--QFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCL-M--KVLHIDLWKC   84 (530)
T ss_dssp             TCHHHHHHHHH-HHHSSCHHHHHHHHHHHHT--TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHT-T--TCCCHHHHHH
T ss_pred             CCHHHHHHHHH-HHHhCCHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-h--cCCChHHHHH
Confidence            37789999998 4889999999999999865  233467789999999999999999999999998 3  3478777776


Q ss_pred             HHHHH------------------hcC-------CCchhhHHHHHHHHHh---------ccChhHHHHHHccCCCCCCC
Q 047113           94 TVDLL------------------ATG-------ETEPYVWGALLGACRI---------HHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        94 li~~~------------------~~~-------~p~~~~~~~li~~~~~---------~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ++...                  -+.       .++...|...+.-..+         .|++++|+.+|++..+ .|.
T Consensus        85 ~~~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~-~P~  161 (530)
T 2ooe_A           85 YLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCV-NPM  161 (530)
T ss_dssp             HHHHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTT-SCC
T ss_pred             HHHHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHh-chh
Confidence            65411                  111       2344577777765554         7899999999999877 353

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.89  E-value=9.8e-05  Score=43.75  Aligned_cols=103  Identities=17%  Similarity=0.055  Sum_probs=73.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +...|..+-..+.+.|++++|...|++... .. +.+...+..+-.++.+.|++++|...++... .  +.|+.......
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--~~p~~~~~~~~   77 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLIT-AQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGL-R--YTSTAEHVAIR   77 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-T--SCSSTTSHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHH-H--hCCCccHHHHH
Confidence            456788899999999999999999999866 32 2367888999999999999999999999998 2  34431000001


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                                ...+..+-.++...|++++|...++++.
T Consensus        78 ----------~~~~~~~~~~~~~~~~~~~a~~~~~~~~  105 (111)
T 2l6j_A           78 ----------SKLQYRLELAQGAVGSVQIPVVEVDELP  105 (111)
T ss_dssp             ----------HHHHHHHHHHHHHHHCCCCCSSSSSSCS
T ss_pred             ----------HHHHHHHHHHHHHHHhHhhhHhHHHHhH
Confidence                      2233445566666677777666655543

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.87  E-value=0.00014  Score=46.78  Aligned_cols=75  Identities=15%  Similarity=0.084  Sum_probs=65.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+...   +.+...|..+-.++.+.|++++|+..|+....   +.| +...|..+-.++.+.|++++|...|+.
T Consensus        53 ~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~---l~P~~~~~~~~lg~~~~~lg~~~eA~~~~~~  129 (151)
T 3gyz_A           53 EEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFA---LGKNDYTPVFHTGQCQLRLKAPLKAKECFEL  129 (151)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSSSCCHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHh---hCCCCcHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            57888888663   34788999999999999999999999999876   345 577889999999999999999999999


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus       130 al  131 (151)
T 3gyz_A          130 VI  131 (151)
T ss_dssp             HH
T ss_pred             HH
Confidence            98

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.86  E-value=0.00039  Score=41.84  Aligned_cols=76  Identities=17%  Similarity=0.155  Sum_probs=63.3

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+...|++++|...++.... .. +.+...+..+...+...|+++.|...++..
T Consensus        29 ~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  106 (131)
T 2vyi_A           29 EAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAIC-ID-PAYSKAYGRMGLALSSLNKHVEAVAYYKKA  106 (131)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHh-cC-ccCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            46777777542   34678899999999999999999999999876 32 235778889999999999999999999998


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       107 ~  107 (131)
T 2vyi_A          107 L  107 (131)
T ss_dssp             H
T ss_pred             H
Confidence            8

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.85  E-value=0.00034  Score=42.06  Aligned_cols=77  Identities=13%  Similarity=0.078  Sum_probs=64.5

Q ss_pred             CchHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            1 MDDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         1 ~~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      +++|.+.|+...   +.+...|..+-..+.+.|++++|...|+.... .. +.+...|..+-.++...|+++.|...|+.
T Consensus         1 ~~~a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~   78 (115)
T 2kat_A            1 MQAITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALD-FD-PTYSVAWKWLGKTLQGQGDRAGARQAWES   78 (115)
T ss_dssp             CCCHHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH-HC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            467788888553   34678899999999999999999999999876 33 23577889999999999999999999998


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus        79 al   80 (115)
T 2kat_A           79 GL   80 (115)
T ss_dssp             HH
T ss_pred             HH
Confidence            87

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.84  E-value=0.00039  Score=42.15  Aligned_cols=92  Identities=15%  Similarity=0.032  Sum_probs=70.6

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...|++... .. +.+...+..+-.++.+.|+++.|...++..
T Consensus        33 ~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  110 (133)
T 2lni_A           33 PQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQ-LE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKA  110 (133)
T ss_dssp             HHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHH-hC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            57888888653   34678899999999999999999999999876 33 236778899999999999999999999998


Q ss_pred             hhhcCcCc-cHHHHHHHHHHH
Q 047113           79 VHDFQLDL-NLEHYGITVDLL   98 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~   98 (145)
                      . .  ..| +...+..+..++
T Consensus       111 ~-~--~~p~~~~~~~~l~~~~  128 (133)
T 2lni_A          111 L-D--LDSSCKEAADGYQRCM  128 (133)
T ss_dssp             H-H--HCGGGTHHHHHHHHHH
T ss_pred             H-H--hCCCchHHHHHHHHHH
Confidence            8 3  233 334444444433

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=97.83  E-value=0.00036  Score=45.37  Aligned_cols=124  Identities=9%  Similarity=-0.133  Sum_probs=87.7

Q ss_pred             chHHHHhccCCC---CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHH-hhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID---KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFA-CSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~---~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~-~~~~~~~~~a~~~~~~   77 (145)
                      ++|...|+....   .+...|..+-.++.+.|++++|...|+.... .  .|+...+...... +.+.+....+...++.
T Consensus        23 ~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~-~--~p~~~~~~~~~~~~~~~~~~~~~a~~~~~~   99 (176)
T 2r5s_A           23 AQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPL-E--YQDNSYKSLIAKLELHQQAAESPELKRLEQ   99 (176)
T ss_dssp             HHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCG-G--GCCHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhh-c--cCChHHHHHHHHHHHHhhcccchHHHHHHH
Confidence            578888887653   4678899999999999999999999999765 2  3444333222111 1222233346777777


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC----------------CCc---hhhHHHHHHHHHhccChhHHHHHHccC
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG----------------ETE---PYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~---~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                      .. .  ..| +...+..+..+|.+.                .|+   ...+..+...+...|+.++|...+++.
T Consensus       100 al-~--~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A          100 EL-A--ANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             HH-H--HSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             HH-H--hCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHH
Confidence            76 2  355 477788888777766                443   458999999999999999999988764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.81  E-value=0.00068  Score=45.85  Aligned_cols=136  Identities=12%  Similarity=-0.051  Sum_probs=89.5

Q ss_pred             chHHHHhccCCC--Cc----hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH-HHHHHHHHHhh-----------
Q 047113            2 DDAERIFGGIID--KN----VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN-VTFLSILFACS-----------   63 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~----~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~-~~~~~ll~~~~-----------   63 (145)
                      ++|.+.|+.+..  |+    ...+..+..++.+.|++++|...|++..+...-.+.. ..+-.+-.++.           
T Consensus        21 ~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~  100 (225)
T 2yhc_A           21 RQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFF  100 (225)
T ss_dssp             HHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhh
Confidence            578888887642  32    2468888999999999999999999987612222221 12322222222           


Q ss_pred             -------ccchHHHHHHHHHHhhhhcCcCcc-HHHHH-----------------HHHHHHhcC----------------C
Q 047113           64 -------YSGLIEEGIKVFDIMVHDFQLDLN-LEHYG-----------------ITVDLLATG----------------E  102 (145)
Q Consensus        64 -------~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~-----------------~li~~~~~~----------------~  102 (145)
                             ..|++++|...|+.+...   .|+ ...+.                 .+...|.+.                .
T Consensus       101 ~~~~~~~~~~~~~~A~~~~~~~l~~---~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~  177 (225)
T 2yhc_A          101 GVDRSDRDPQQARAAFSDFSKLVRG---YPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDY  177 (225)
T ss_dssp             -------CCHHHHHHHHHHHHHHTT---CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             ccchhhcCcHHHHHHHHHHHHHHHH---CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHC
Confidence                   368999999999999832   232 22221                 112222222                4


Q ss_pred             Cch----hhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113          103 TEP----YVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus       103 p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      |+.    ..+..+..+|.+.|+.++|...++.+....|++..
T Consensus       178 p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~~~  219 (225)
T 2yhc_A          178 PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTLE  219 (225)
T ss_dssp             TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCCCC
T ss_pred             cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCchh
Confidence            432    46888899999999999999999988887776544

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.79  E-value=0.00029  Score=49.73  Aligned_cols=123  Identities=7%  Similarity=-0.123  Sum_probs=92.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHH-HHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFL-SILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~-~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+...   +.+...+..+...+.+.|++++|...|++...   ..|+..... .....+.+.+..+.+...+++
T Consensus       134 ~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~---~~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~  210 (287)
T 3qou_A          134 TDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPL---QDQDTRYQGLVAQIELLXQAADTPEIQQLQQ  210 (287)
T ss_dssp             HHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCG---GGCSHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCch---hhcchHHHHHHHHHHHHhhcccCccHHHHHH
Confidence            56788888653   34677899999999999999999999999755   345544332 223335667777778888887


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC----------------CCc---hhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG----------------ETE---PYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~---~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      .. .  ..| +...+..+..+|...                .|+   ...+..+...+...|+.++|...+++
T Consensus       211 al-~--~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~  280 (287)
T 3qou_A          211 QV-A--ENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXYRR  280 (287)
T ss_dssp             HH-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HH-h--cCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            77 2  344 577788888887766                443   56899999999999999999988875

>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=97.78  E-value=0.00045  Score=48.63  Aligned_cols=75  Identities=12%  Similarity=0.003  Sum_probs=63.4

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..-   +.+...|..+-.++.+.|++++|...|+...+   +.| +...+..+-.++...|++++|...|+.
T Consensus        21 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~   97 (281)
T 2c2l_A           21 PEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE---LDGQSVKAHFFLGQCQLEMESYDEAIANLQR   97 (281)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT---SCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            46777777542   34778899999999999999999999999755   445 577889999999999999999999998


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus        98 al   99 (281)
T 2c2l_A           98 AY   99 (281)
T ss_dssp             HH
T ss_pred             HH
Confidence            77

>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=97.76  E-value=4.2e-05  Score=56.35  Aligned_cols=105  Identities=9%  Similarity=-0.048  Sum_probs=79.7

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhc-------------CCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCS-------------DGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF   82 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~-------------~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~   82 (145)
                      ..|..+-..+.+.|++++|+..|++..+..             ...| +...|+.+-.++.+.|++++|...+++.. . 
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al-~-  301 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEAL-E-  301 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-T-
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHH-H-
Confidence            358888899999999999999999865300             1233 46688889999999999999999999998 3 


Q ss_pred             CcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           83 QLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        83 ~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                       +.|+                +...|..+-.+|...|++++|+..+++..++.|+++.
T Consensus       302 -~~p~----------------~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~  342 (370)
T 1ihg_A          302 -IDPS----------------NTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKA  342 (370)
T ss_dssp             -TCTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             -hCch----------------hHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHH
Confidence             3442                4455666677777888888888888887777776543

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.76  E-value=0.00027  Score=51.11  Aligned_cols=97  Identities=11%  Similarity=-0.056  Sum_probs=75.9

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGIT   94 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~l   94 (145)
                      ...|..+-.++.+.|++++|+..|+...+ .. +.+...|..+-.++...|+++.|...|++.. .  +.| +...+..+
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~-~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al-~--l~P~~~~a~~~l  270 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALE-LD-SNNEKGLSRRGEAHLAVNDFELARADFQKVL-Q--LYPNNKAAKTQL  270 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCSSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H--HCCCCHHHHHHH
Confidence            47899999999999999999999999876 33 2368899999999999999999999999998 3  345 56777777


Q ss_pred             HHHHhcC----CCchhhHHHHHHHHHh
Q 047113           95 VDLLATG----ETEPYVWGALLGACRI  117 (145)
Q Consensus        95 i~~~~~~----~p~~~~~~~li~~~~~  117 (145)
                      ..++.+.    .-....|..++..+..
T Consensus       271 ~~~~~~~~~~~~a~~~~~~~~~~~~~~  297 (336)
T 1p5q_A          271 AVCQQRIRRQLAREKKLYANMFERLAE  297 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            7777765    2223456666655544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.75  E-value=0.00019  Score=52.23  Aligned_cols=118  Identities=6%  Similarity=-0.185  Sum_probs=86.7

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-----cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-----NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-   86 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-----~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-   86 (145)
                      ..+|..+-..|...|++++|...+.+......-.+     ...+++.+-..+...|+++.|...++......   +-.+ 
T Consensus       143 a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  222 (383)
T 3ulq_A          143 AEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQL  222 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHH
Confidence            45799999999999999999999988653111112     24578888899999999999999998877321   1111 


Q ss_pred             cHHHHHHHHHHHhcC---------------------C-Cc-hhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           87 NLEHYGITVDLLATG---------------------E-TE-PYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        87 ~~~~~~~li~~~~~~---------------------~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ...++..+..+|.+.                     . |. ..++..+-..|.+.|++++|...+++..+
T Consensus       223 ~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          223 MGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            134667777777665                     1 32 34788888999999999999999987665

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.75  E-value=0.00033  Score=50.54  Aligned_cols=118  Identities=10%  Similarity=-0.029  Sum_probs=86.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-c
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-N   87 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-~   87 (145)
                      ..+|..+...+...|++++|...|++......-.++    ...+..+-..+...|+++.|...++......   +-.+ .
T Consensus       187 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  266 (406)
T 3sf4_A          187 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE  266 (406)
T ss_dssp             HHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHH
Confidence            357889999999999999999999986531111122    3378888889999999999999999876211   1111 1


Q ss_pred             HHHHHHHHHHHhcC-------------------CCc----hhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           88 LEHYGITVDLLATG-------------------ETE----PYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        88 ~~~~~~li~~~~~~-------------------~p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..++..+...|.+.                   .++    ..++..+-..|...|++++|...+++..+
T Consensus       267 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          267 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            55667777777665                   222    45788888999999999999999887655

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.74  E-value=0.00062  Score=43.26  Aligned_cols=76  Identities=13%  Similarity=0.068  Sum_probs=64.6

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..   .+.+...|..+-.++.+.|++++|...|+.... .  .| +...+..+-.++...|++++|...|+.
T Consensus        38 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-l--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  114 (148)
T 2vgx_A           38 EDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAV-M--DIXEPRFPFHAAECLLQXGELAEAESGLFL  114 (148)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--STTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-c--CCCCchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            5678888865   345788999999999999999999999999876 3  34 677888899999999999999999999


Q ss_pred             hhh
Q 047113           78 MVH   80 (145)
Q Consensus        78 m~~   80 (145)
                      ...
T Consensus       115 al~  117 (148)
T 2vgx_A          115 AQE  117 (148)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            883

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=97.73  E-value=4.8e-05  Score=58.55  Aligned_cols=107  Identities=14%  Similarity=0.001  Sum_probs=74.3

Q ss_pred             cCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC-----
Q 047113           29 HGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG-----  101 (145)
Q Consensus        29 ~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~-----  101 (145)
                      .|++++|...|++..+   ..| +...+..+-..+.+.|++++|...+++.. +  ..| +...|..+..+|.+.     
T Consensus         2 ~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--~~p~~~~~~~~lg~~~~~~g~~~~   75 (568)
T 2vsy_A            2 TADGPRELLQLRAAVR---HRPQDFVAWLMLADAELGMGDTTAGEMAVQRGL-A--LHPGHPEAVARLGRVRWTQQRHAE   75 (568)
T ss_dssp             ----------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-T--TSTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             CccHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCCCCHHHHHHHHHHHHHCCCHHH
Confidence            4789999999998754   345 57789999999999999999999999998 3  344 577888888888766     


Q ss_pred             ------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          102 ------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       102 ------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                                  +.+...|..+-..|.+.|++++|...+++..+..|+++..
T Consensus        76 A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~  127 (568)
T 2vsy_A           76 AAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYI  127 (568)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH
Confidence                        4456789999999999999999999999998888876543

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.73  E-value=8.3e-05  Score=52.00  Aligned_cols=121  Identities=12%  Similarity=-0.010  Sum_probs=86.3

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-c
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-N   87 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-~   87 (145)
                      ..+|..+...+...|++++|...|++....   .+-.+ ....+..+...+...|+++.|...++......   +-.+ .
T Consensus       183 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  262 (338)
T 3ro2_A          183 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE  262 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHH
Confidence            347888999999999999999999986531   11111 13377888888999999999999998876321   1111 1


Q ss_pred             HHHHHHHHHHHhcC-------------------CC----chhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           88 LEHYGITVDLLATG-------------------ET----EPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        88 ~~~~~~li~~~~~~-------------------~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      ..++..+...|.+.                   ..    ...++..+...|.+.|++++|...+++..++.+
T Consensus       263 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  334 (338)
T 3ro2_A          263 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISR  334 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence            55666677777665                   11    134778888999999999999999998766543

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.69  E-value=0.0004  Score=50.54  Aligned_cols=117  Identities=13%  Similarity=-0.011  Sum_probs=85.1

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHh---hcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCc--Cc-cHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIH---CSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQL--DL-NLE   89 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~---~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~--~~-~~~   89 (145)
                      .+|+.+-..|.+.|++++|...|++...   ..+-.| ...++..+-..+.+.|+++.|...+++......-  .| ...
T Consensus       225 ~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  304 (383)
T 3ulq_A          225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLS  304 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            4799999999999999999999988643   014424 4668899999999999999999999987732111  12 223


Q ss_pred             HHHHHHHHHhcC------------------C-CchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           90 HYGITVDLLATG------------------E-TEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        90 ~~~~li~~~~~~------------------~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .+..+...|.+.                  . .....+..+-..|...|++++|...+++..+
T Consensus       305 ~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          305 EFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            344455555443                  1 2234677888999999999999999988665

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.69  E-value=0.00074  Score=45.66  Aligned_cols=125  Identities=8%  Similarity=-0.094  Sum_probs=79.0

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccH-HHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNL-EHYGI   93 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~   93 (145)
                      ...+-.+...+.+.|++++|...|+.+.....-.|. ...+..+..++.+.|+++.|...|+.+.....-.+.. ..+..
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~   83 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHH
Confidence            345666778899999999999999998761222222 3577778889999999999999999998332212221 13333


Q ss_pred             HHHHHhcC-CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           94 TVDLLATG-ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        94 li~~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      +..+|.+. ......|..+-..+...|++++|...|+++.+..|+++.
T Consensus        84 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~  131 (225)
T 2yhc_A           84 RGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQY  131 (225)
T ss_dssp             HHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTT
T ss_pred             HHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChh
Confidence            33334332 111122333444555678999999999999998887764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.68  E-value=0.001  Score=42.55  Aligned_cols=76  Identities=14%  Similarity=0.097  Sum_probs=64.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+-.++.+.|++++|+..|+.... .. +-+...|..+-.++...|+++.|...|++.
T Consensus        28 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a  105 (164)
T 3sz7_A           28 SKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATV-VD-PKYSKAWSRLGLARFDMADYKGAKEAYEKG  105 (164)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            56777777553   34778999999999999999999999999876 33 225788999999999999999999999999


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       106 l  106 (164)
T 3sz7_A          106 I  106 (164)
T ss_dssp             H
T ss_pred             H
Confidence            8

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.68  E-value=0.0013  Score=38.64  Aligned_cols=89  Identities=18%  Similarity=0.129  Sum_probs=68.7

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+...+.+.|++++|...+++... .. +.+...+..+..++...|+++.|...++..
T Consensus        21 ~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~   98 (118)
T 1elw_A           21 DDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVD-LK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEG   98 (118)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHH-hC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            46777777552   34678899999999999999999999999876 32 236778889999999999999999999998


Q ss_pred             hhhcCcCc-cHHHHHHHH
Q 047113           79 VHDFQLDL-NLEHYGITV   95 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li   95 (145)
                      . .  ..| +...+..+.
T Consensus        99 ~-~--~~~~~~~~~~~l~  113 (118)
T 1elw_A           99 L-K--HEANNPQLKEGLQ  113 (118)
T ss_dssp             H-T--TCTTCHHHHHHHH
T ss_pred             H-H--cCCCCHHHHHHHH
Confidence            8 3  334 344444443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.68  E-value=0.00056  Score=48.68  Aligned_cols=118  Identities=9%  Similarity=-0.113  Sum_probs=78.9

Q ss_pred             chHHHHhccCCC--CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc--HHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGIID--KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN--NVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.++|+.+..  |+-...-.+-..+.+.+++++|+..|+.... .. .|.  ...+..+-.++.+.|++++|+..|++
T Consensus       119 ~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~-~~-d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~  196 (282)
T 4f3v_A          119 ADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGK-WP-DKFLAGAAGVAHGVAAANLALFTEAERRLTE  196 (282)
T ss_dssp             HHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGG-CS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhc-cC-CcccHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            577888887753  4222555555677888888888888875433 11 111  22556666777888888888888887


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      .. .....|..               ....+...-.++.+.|+.++|...|+++....|+
T Consensus       197 a~-~g~~~P~~---------------~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~  240 (282)
T 4f3v_A          197 AN-DSPAGEAC---------------ARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE  240 (282)
T ss_dssp             HH-TSTTTTTT---------------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC
T ss_pred             Hh-cCCCCccc---------------cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc
Confidence            76 33332321               1224445667788999999999999999888876

>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=97.67  E-value=6.8e-05  Score=56.98  Aligned_cols=102  Identities=8%  Similarity=-0.032  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      |..+-..+.+.|++++|...|++..+ .  .| +...|..+-.++.+.|++++|...+++.. +  +.|+          
T Consensus         9 ~~~lg~~~~~~g~~~~A~~~~~~Al~-~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--l~p~----------   72 (477)
T 1wao_1            9 LKTQANDYFKAKDYENAIKFYSQAIE-L--NPSNAIYYGNRSLAYLRTECYGYALGDATRAI-E--LDKK----------   72 (477)
T ss_dssp             SSSSSSSTTTTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--SCTT----------
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHH-h--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHH-H--hCCC----------
Confidence            33444556788999999999999876 3  45 57899999999999999999999999998 3  2332          


Q ss_pred             HhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           98 LATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        98 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                            +...|..+-.+|...|++++|...+++..+..|+++..+
T Consensus        73 ------~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~p~~~~~~  111 (477)
T 1wao_1           73 ------YIKGYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAK  111 (477)
T ss_dssp             ------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCTTHH
T ss_pred             ------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHH
Confidence                  556777888899999999999999999988888776543

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.67  E-value=0.00071  Score=39.59  Aligned_cols=76  Identities=16%  Similarity=0.074  Sum_probs=63.4

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC--cHHHHHHHHHHhhcc-chHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP--NNVTFLSILFACSYS-GLIEEGIKVF   75 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p--~~~~~~~ll~~~~~~-~~~~~a~~~~   75 (145)
                      ++|...|+...   +.+...|..+...+.+.|++++|...|++..+ .. +.  +...+..+...+.+. |++++|.+.+
T Consensus        23 ~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~  100 (112)
T 2kck_A           23 TESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVIN-VI-EDEYNKDVWAAKADALRYIEGKEVEAEIAE  100 (112)
T ss_dssp             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-TS-CCTTCHHHHHHHHHHHTTCSSCSHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHH-hC-cccchHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            46777777543   34677899999999999999999999999876 32 22  577889999999999 9999999999


Q ss_pred             HHhh
Q 047113           76 DIMV   79 (145)
Q Consensus        76 ~~m~   79 (145)
                      +...
T Consensus       101 ~~~~  104 (112)
T 2kck_A          101 ARAK  104 (112)
T ss_dssp             HHHG
T ss_pred             HHHh
Confidence            9998

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=97.66  E-value=0.00081  Score=47.26  Aligned_cols=114  Identities=9%  Similarity=-0.085  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCC-Cc----HHHHHHHHHHhhccchHHHHHHHHHHhhhh---c-CcCcc-H
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGK-PN----NVTFLSILFACSYSGLIEEGIKVFDIMVHD---F-QLDLN-L   88 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~-p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~-~~~~~-~   88 (145)
                      +..+...+...|++++|+..|..... .... ++    ...++.+-..+...|+++.|...|+.....   . +..+. .
T Consensus       118 ~~~l~~~~~~~~~~~~Ai~~~~~al~-~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (293)
T 3u3w_A          118 QYYVAAYVLKKVDYEYCILELKKLLN-QQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDV  196 (293)
T ss_dssp             HHHHHHHHTTSSCHHHHHHHHHHHHH-TCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHH
T ss_pred             HHHHHHHHHcccCHHHHHHHHHHHHH-HhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHH
Confidence            34466666677788888888888765 3222 23    236788888888888888888888887721   1 22222 3


Q ss_pred             HHHHHHHHHHhcC----------------------CCc-hhhHHHHHHHHHhccC-hhHHHHHHccCCC
Q 047113           89 EHYGITVDLLATG----------------------ETE-PYVWGALLGACRIHHN-VKIGELVAKDPFH  133 (145)
Q Consensus        89 ~~~~~li~~~~~~----------------------~p~-~~~~~~li~~~~~~g~-~~~a~~~~~~~~~  133 (145)
                      .+|..+...|.+.                      .+. ..+|..+-.+|.+.|+ +++|...+++...
T Consensus       197 ~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          197 KVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            4666677777665                      111 4577777888888884 5777777766443

>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=97.66  E-value=0.0002  Score=44.38  Aligned_cols=89  Identities=8%  Similarity=-0.031  Sum_probs=66.4

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC--CCCc----HHHHHHHHHHhhccchHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSD--GKPN----NVTFLSILFACSYSGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~--~~p~----~~~~~~ll~~~~~~~~~~~a~   72 (145)
                      ++|.+.|++.   .+.+...|+.+-.+|.+.|++++|+..|+...+ ..  ..++    ..+|..+-.++...|+++.|.
T Consensus        25 ~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~-~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~  103 (127)
T 4gcn_A           25 EKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVE-VGRETRADYKLIAKAMSRAGNAFQKQNDLSLAV  103 (127)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHH-hCcccchhhHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            5677888754   345788999999999999999999999998754 21  1111    246777788889999999999


Q ss_pred             HHHHHhhhhcCcCccHHHHHHH
Q 047113           73 KVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        73 ~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      +.|++.. .  ..||..+...|
T Consensus       104 ~~~~kal-~--~~~~~~~~~~l  122 (127)
T 4gcn_A          104 QWFHRSL-S--EFRDPELVKKV  122 (127)
T ss_dssp             HHHHHHH-H--HSCCHHHHHHH
T ss_pred             HHHHHHH-h--hCcCHHHHHHH
Confidence            9999887 3  35665554443

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.65  E-value=0.00072  Score=50.18  Aligned_cols=119  Identities=8%  Similarity=-0.083  Sum_probs=81.3

Q ss_pred             CchhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cH
Q 047113           14 KNVVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NL   88 (145)
Q Consensus        14 ~~~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~   88 (145)
                      .+...+..+...+..    .|++++|..++++... .. +.+...+..+-..+...|+++.|...+++.. .  ..| +.
T Consensus       207 ~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~-~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~--~~p~~~  281 (472)
T 4g1t_A          207 DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALE-KA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKAL-E--YIPNNA  281 (472)
T ss_dssp             SCHHHHHHHHHHHHHCC------CHHHHHHHHHHH-HC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HSTTCH
T ss_pred             cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH-hC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHH-H--hCCChH
Confidence            345566665555554    3567788888887654 22 2356678888888999999999999998887 3  334 45


Q ss_pred             HHHHHHHHHHhcC------------------------------------CCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           89 EHYGITVDLLATG------------------------------------ETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        89 ~~~~~li~~~~~~------------------------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      ..+..+..+|...                                    +.+..+|..+-..|...|++++|...|++..
T Consensus       282 ~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL  361 (472)
T 4g1t_A          282 YLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEF  361 (472)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHH
Confidence            5666555554321                                    4455688888899999999999999999877


Q ss_pred             CCCCC
Q 047113          133 HLDPK  137 (145)
Q Consensus       133 ~~~~~  137 (145)
                      +..|+
T Consensus       362 ~~~~~  366 (472)
T 4g1t_A          362 SKELT  366 (472)
T ss_dssp             HSCCC
T ss_pred             hcCCC
Confidence            76653

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.65  E-value=0.00014  Score=52.78  Aligned_cols=102  Identities=12%  Similarity=0.024  Sum_probs=53.9

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      .|+.+-.++.+.|++++|+..|+...+ .. +-+...|..+-.++...|+++.|...|++..   .+.|+          
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~-~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al---~l~p~----------  296 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLT-EE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQ---KYAPD----------  296 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTT---C--------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---HHCCC----------
Confidence            789999999999999999999999866 32 2367899999999999999999999999988   23443          


Q ss_pred             HhcCCCchhhHHHHHHH-HHhccChhHHHHHHccCCCCCCCCCC
Q 047113           98 LATGETEPYVWGALLGA-CRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        98 ~~~~~p~~~~~~~li~~-~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                            +...+..+... ....+..+++...|.++....|.++.
T Consensus       297 ------~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~~p~~~~  334 (338)
T 2if4_A          297 ------DKAIRRELRALAEQEKALYQKQKEMYKGIFKGKDEGGA  334 (338)
T ss_dssp             --------------------------------------------
T ss_pred             ------CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCC
Confidence                  22333333333 23456778888999999888776543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.64  E-value=0.00089  Score=41.90  Aligned_cols=76  Identities=17%  Similarity=0.115  Sum_probs=64.1

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|.+.|+...   +.+...|..+-.++.+.|++++|...|+.... .. +-+...+..+-.++...|+++.|...|+..
T Consensus        35 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a  112 (142)
T 2xcb_A           35 DDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGAL-MD-INEPRFPFHAAECHLQLGDLDGAESGFYSA  112 (142)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-cC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            57888888653   34778899999999999999999999999876 33 235678888889999999999999999998


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       113 l  113 (142)
T 2xcb_A          113 R  113 (142)
T ss_dssp             H
T ss_pred             H
Confidence            8

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.63  E-value=0.00028  Score=51.41  Aligned_cols=118  Identities=8%  Similarity=-0.088  Sum_probs=86.0

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHHHHHHHHhhhhcC---cC-cc
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ---LD-LN   87 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~---~~-~~   87 (145)
                      ..+|..+-..+...|++++|...|++......-.++    ...+..+...+...|++++|...++.......   -. ..
T Consensus       223 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  302 (411)
T 4a1s_A          223 GRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVE  302 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            357889999999999999999999986541110112    23788888999999999999999988773211   11 12


Q ss_pred             HHHHHHHHHHHhcC-------------------CC----chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           88 LEHYGITVDLLATG-------------------ET----EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        88 ~~~~~~li~~~~~~-------------------~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..++..+..+|.+.                   .+    ...++..+...|...|++++|...+++..+
T Consensus       303 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          303 AQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            55667777777665                   11    134788888999999999999999987654

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.63  E-value=0.00044  Score=49.11  Aligned_cols=122  Identities=7%  Similarity=-0.097  Sum_probs=85.5

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-c
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-N   87 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-~   87 (145)
                      ..+|+.+...|.+.|++++|...|++....   .|-.. -..+++.+-..+.. |+++.|...+++.....   +-.+ .
T Consensus        76 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~  154 (307)
T 2ifu_A           76 AKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQA  154 (307)
T ss_dssp             HHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHH
Confidence            357889999999999999999999875431   12111 24577888888888 99999999998877211   1111 1


Q ss_pred             HHHHHHHHHHHhcC-------------------CCc----hhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           88 LEHYGITVDLLATG-------------------ETE----PYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        88 ~~~~~~li~~~~~~-------------------~p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ..++..+...|.+.                   .++    ...+..+...+...|++++|...+++.. ..|...
T Consensus       155 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~~p~~~  228 (307)
T 2ifu_A          155 AELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-SIPGFS  228 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TSTTST
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-CCCCCC
Confidence            45677777777765                   111    2356666777778899999999999988 777544

>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=97.62  E-value=0.00038  Score=41.93  Aligned_cols=91  Identities=10%  Similarity=0.028  Sum_probs=68.5

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCC--CCc----HHHHHHHHHHhhccchHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDG--KPN----NVTFLSILFACSYSGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~--~p~----~~~~~~ll~~~~~~~~~~~a~   72 (145)
                      ++|...|+...   +.+...|..+...+.+.|++++|...|+.... ..-  .++    ...+..+..++...|+++.|.
T Consensus        21 ~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~   99 (131)
T 1elr_A           21 DTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIE-VGRENREDYRQIAKAYARIGNSYFKEEKYKDAI   99 (131)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHh-hccccchhHHHHHHHHHHHHHHHHHhccHHHHH
Confidence            46777777542   34677899999999999999999999999765 321  122    678888899999999999999


Q ss_pred             HHHHHhhhhcCcCccHHHHHHHHH
Q 047113           73 KVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        73 ~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      ..|+... .  ..|+...+..+..
T Consensus       100 ~~~~~~~-~--~~~~~~~~~~l~~  120 (131)
T 1elr_A          100 HFYNKSL-A--EHRTPDVLKKCQQ  120 (131)
T ss_dssp             HHHHHHH-H--HCCCHHHHHHHHH
T ss_pred             HHHHHHH-H--hCCCHHHHHHHHH
Confidence            9999998 3  3345555444443

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.61  E-value=0.00045  Score=50.25  Aligned_cols=119  Identities=6%  Similarity=-0.134  Sum_probs=86.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC----CCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSD----GKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-   86 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~----~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-   86 (145)
                      ..+|..+-..|...|++++|...+.+......    ..+ ...+++.+-..+...|+++.|...++......   +-.+ 
T Consensus       141 a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~  220 (378)
T 3q15_A          141 AEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRF  220 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHH
Confidence            45788999999999999999999988643111    122 24578888889999999999999998877311   1111 


Q ss_pred             cHHHHHHHHHHHhcC---------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           87 NLEHYGITVDLLATG---------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        87 ~~~~~~~li~~~~~~---------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      ...++..+..+|...                     .| ...++..+-..|.+.|++++|...+++..+.
T Consensus       221 ~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  290 (378)
T 3q15_A          221 IAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDH  290 (378)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            234566666666554                     22 3457888889999999999999999987764

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.61  E-value=0.00041  Score=42.56  Aligned_cols=75  Identities=9%  Similarity=0.116  Sum_probs=63.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|...|+...   +.+...|..+-.++.+.|++++|+..|++..+   +.| +...+..+-.++.+.|++++|...+++
T Consensus        34 ~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~---l~P~~~~~~~~la~~~~~~g~~~~A~~~~~~  110 (121)
T 1hxi_A           34 AEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARM---LDPKDIAVHAALAVSHTNEHNANAALASLRA  110 (121)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            56777777553   34778899999999999999999999999866   345 577888999999999999999999999


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus       111 al  112 (121)
T 1hxi_A          111 WL  112 (121)
T ss_dssp             HH
T ss_pred             HH
Confidence            87

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.61  E-value=0.00078  Score=39.73  Aligned_cols=83  Identities=11%  Similarity=0.067  Sum_probs=62.7

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      .+...|..+-.++.+.|++++|...|+...+ .. +-+...|..+-.++...|++++|...+++......-.++.....-
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~   82 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVE-TD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSE   82 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHH
Confidence            3677899999999999999999999999876 33 225678899999999999999999999988732222334444444


Q ss_pred             HHHHH
Q 047113           94 TVDLL   98 (145)
Q Consensus        94 li~~~   98 (145)
                      +...+
T Consensus        83 l~~~l   87 (100)
T 3ma5_A           83 LQDAK   87 (100)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            43333

>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=97.61  E-value=0.0012  Score=56.41  Aligned_cols=117  Identities=15%  Similarity=0.156  Sum_probs=79.5

Q ss_pred             chHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhh
Q 047113            2 DDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus         2 ~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      ++|.++.++.  .+..+|..+-.++-+.|++++|...|..-       -|...|.-+..+|.+.|+++++.+.+.... +
T Consensus      1093 drAiE~Aerv--n~p~vWsqLAKAql~~G~~kEAIdsYiKA-------dD~say~eVa~~~~~lGkyEEAIeyL~mAr-k 1162 (1630)
T 1xi4_A         1093 DRAYEFAERC--NEPAVWSQLAKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMAR-K 1162 (1630)
T ss_pred             HHHHHHHHhc--CCHHHHHHHHHHHHhCCCHHHHHHHHHhc-------CChHHHHHHHHHHHHcCCHHHHHHHHHHHH-h
Confidence            3455555543  34678999999999999999999999542       477788889999999999999999998766 3


Q ss_pred             cCcCccHHHHHHHHHHHhcC-----------CCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           82 FQLDLNLEHYGITVDLLATG-----------ETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        82 ~~~~~~~~~~~~li~~~~~~-----------~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      ..  ++....+.++.+|++.           .++...|..+-..|...|++++|..+|..
T Consensus      1163 ~~--~e~~Idt~LafaYAKl~rleele~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y~k 1220 (1630)
T 1xi4_A         1163 KA--RESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNN 1220 (1630)
T ss_pred             hc--ccccccHHHHHHHHhhcCHHHHHHHHhCCCHHHHHHHHHHHHhcCCHHHHHHHHHh
Confidence            32  2222223366666665           44444445555555555555555555554

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=97.60  E-value=0.0019  Score=45.30  Aligned_cols=116  Identities=7%  Similarity=-0.039  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH----HHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc----HHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV----TFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN----LEH   90 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~----~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~----~~~   90 (145)
                      +...+..+.+.|++++|...+++........|+..    .+..+...+...++++.|...++.......-.++    ...
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHH
Confidence            44457888999999999999999876233444422    3445677778888999999999999831111223    346


Q ss_pred             HHHHHHHHhcC-------------------C-C----chhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           91 YGITVDLLATG-------------------E-T----EPYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        91 ~~~li~~~~~~-------------------~-p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      ++.+..+|.+.                   . .    ...++..+...|.+.|++++|...+++..++
T Consensus       158 ~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~  225 (293)
T 3u3w_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEI  225 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            88888888765                   1 1    1237888999999999999999999887663

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.59  E-value=0.0011  Score=40.35  Aligned_cols=75  Identities=13%  Similarity=0.055  Sum_probs=64.1

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..   .+.+...|..+-.++.+.|++++|...|+...+ .  .| +...|..+-.++...|+++.|...|+.
T Consensus        21 ~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~-~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~   97 (126)
T 3upv_A           21 PNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIE-K--DPNFVRAYIRKATAQIAVKEYASALETLDA   97 (126)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHH-h--CCCcHHHHHHHHHHHHHHhCHHHHHHHHHH
Confidence            4677777754   234778999999999999999999999999876 3  35 577899999999999999999999998


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus        98 al   99 (126)
T 3upv_A           98 AR   99 (126)
T ss_dssp             HH
T ss_pred             HH
Confidence            88

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.57  E-value=0.00053  Score=42.67  Aligned_cols=116  Identities=11%  Similarity=-0.001  Sum_probs=63.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-cHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-NLE   89 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-~~~   89 (145)
                      +|..+-..+...|++++|...|++......-.++    ...+..+-..+...|++++|...++......   +-.+ ...
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            4556666666666666666666654330100011    1355555666666666666666666554211   1011 122


Q ss_pred             HHHHHHHHHhcC-------------------C----CchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           90 HYGITVDLLATG-------------------E----TEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        90 ~~~~li~~~~~~-------------------~----p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .+..+..+|...                   .    ....++..+-..+...|++++|...+++..+
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            333333333333                   1    1234677788888999999999998887554

>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=97.56  E-value=0.0011  Score=44.48  Aligned_cols=123  Identities=6%  Similarity=-0.149  Sum_probs=90.5

Q ss_pred             hHHHHhccCC-CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc----hHHHHHHHHHH
Q 047113            3 DAERIFGGII-DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSG----LIEEGIKVFDI   77 (145)
Q Consensus         3 ~A~~~f~~m~-~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~----~~~~a~~~~~~   77 (145)
                      +|.+.|+..- ..+...+..|-..|...+++++|...|+...+ .|   +...+..+-..+.. +    ++++|...|++
T Consensus         4 eA~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~-~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~   78 (212)
T 3rjv_A            4 EPGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAA-QG---DGDALALLAQLKIR-NPQQADYPQARQLAEK   78 (212)
T ss_dssp             CTTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-TT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHH-cC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHH
Confidence            4666666543 35777888888888889999999999998877 44   56677777777777 6    88899999988


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhc----C----------------CCc---hhhHHHHHHHHHh----ccChhHHHHHHcc
Q 047113           78 MVHDFQLDLNLEHYGITVDLLAT----G----------------ETE---PYVWGALLGACRI----HHNVKIGELVAKD  130 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~----~----------------~p~---~~~~~~li~~~~~----~g~~~~a~~~~~~  130 (145)
                      .. +.|   +...+..|-..|..    .                .|.   ..++..|-..|..    .+++++|...|++
T Consensus        79 A~-~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~  154 (212)
T 3rjv_A           79 AV-EAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKG  154 (212)
T ss_dssp             HH-HTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHH
T ss_pred             HH-HCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            87 544   45566666666754    1                321   5777888888877    7788999988888


Q ss_pred             CCCC
Q 047113          131 PFHL  134 (145)
Q Consensus       131 ~~~~  134 (145)
                      ..+.
T Consensus       155 A~~~  158 (212)
T 3rjv_A          155 SSSL  158 (212)
T ss_dssp             HHHT
T ss_pred             HHHc
Confidence            7655

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.49  E-value=0.0014  Score=47.64  Aligned_cols=118  Identities=6%  Similarity=0.030  Sum_probs=83.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcC---cCccHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ---LDLNLE   89 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~---~~~~~~   89 (145)
                      ..+++.|-..|.+.|++++|...|.+....   .+-+....++..+-..+.+.|+++.|...+++......   -.....
T Consensus       222 ~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  301 (378)
T 3q15_A          222 AISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKE  301 (378)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            357889999999999999999999886430   13333466888899999999999999999998873222   111233


Q ss_pred             HHHHHHHHHhcC------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           90 HYGITVDLLATG------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        90 ~~~~li~~~~~~------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .+..+-..|...                  .| ....+..+-..|...|++++|...+++..+
T Consensus       302 ~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          302 LFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            344444444332                  11 223566788899999999999999987654

>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=97.45  E-value=0.0012  Score=43.45  Aligned_cols=95  Identities=15%  Similarity=0.092  Sum_probs=66.1

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      ..|..+-.++.+.|++++|...++.... .. +.+...+..+-.++...|+++.|...|+... .  +.|+         
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~--~~p~---------  154 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLK-ID-KNNVKALYKLGVANMYFGFLEEAKENLYKAA-S--LNPN---------  154 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-H--HSTT---------
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHH-hC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHH-H--HCCC---------
Confidence            7899999999999999999999999876 32 3367788999999999999999999999988 3  2342         


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHH-HHHccCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGE-LVAKDPF  132 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~-~~~~~~~  132 (145)
                             +...+..+-..+...|+.+++. ..+..+.
T Consensus       155 -------~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          155 -------NLDIRNSYELCVNKLKEARKKDKLTFGGMF  184 (198)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHHC----------
T ss_pred             -------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence                   3344444555555555555554 3444433

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.45  E-value=0.00017  Score=51.99  Aligned_cols=117  Identities=15%  Similarity=0.140  Sum_probs=76.7

Q ss_pred             chHHHHhccCCC--C-----chhhHHHHHHH--HHHcC--ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHH
Q 047113            2 DDAERIFGGIID--K-----NVVIWSGMIAS--HAIHG--QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEE   70 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-----~~~~~~~li~a--~~~~g--~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~   70 (145)
                      +.|.+.|++|..  |     +-.+.-.|..+  ....|  ++.+|..+|+++..   -.|+..+-..++.++.+.|++++
T Consensus       153 d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~---~~p~~~~~~lLln~~~~~g~~~e  229 (310)
T 3mv2_B          153 STASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQ---TFPTWKTQLGLLNLHLQQRNIAE  229 (310)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHT---TSCSHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH---hCCCcccHHHHHHHHHHcCCHHH
Confidence            678999998864  4     23455555555  33334  99999999999865   23554454566668999999999


Q ss_pred             HHHHHHHhhhhc----C---cCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           71 GIKVFDIMVHDF----Q---LDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        71 a~~~~~~m~~~~----~---~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      |+..++.+....    +   ..|+                |..+...+|-.....|+  +|.+++.++.+..|+.|
T Consensus       230 Ae~~L~~l~~~~p~~~~k~~~~p~----------------~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~P~hp  287 (310)
T 3mv2_B          230 AQGIVELLLSDYYSVEQKENAVLY----------------KPTFLANQITLALMQGL--DTEDLTNQLVKLDHEHA  287 (310)
T ss_dssp             HHHHHHHHHSHHHHTTTCHHHHSS----------------HHHHHHHHHHHHHHTTC--TTHHHHHHHHHTTCCCH
T ss_pred             HHHHHHHHHHhcccccccccCCCC----------------CHHHHHHHHHHHHHhCh--HHHHHHHHHHHhCCCCh
Confidence            999999776221    1   0232                33333233333333455  77888888888888765

>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=97.43  E-value=0.00068  Score=51.09  Aligned_cols=94  Identities=16%  Similarity=0.001  Sum_probs=71.2

Q ss_pred             HcCChHHHHHHHHHhHhh--cCCCC---c-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcC
Q 047113           28 IHGQEREALEAFYLVIHC--SDGKP---N-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        28 ~~g~~~~A~~~~~~m~~~--~~~~p---~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~  101 (145)
                      ..|++++|..++++....  .-+-|   + ..+++.+..+|...|++++|+.++++...            ..-..|+..
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~------------i~~~~lG~~  377 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIK------------PYSKHYPVY  377 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH------------HHHHHSCSS
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHH------------HHHHHcCCC
Confidence            357899999999885321  22333   3 46899999999999999999999998872            122233333


Q ss_pred             CCch-hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113          102 ETEP-YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus       102 ~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .|++ .+++.|-..|...|++++|+.++++..+
T Consensus       378 Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          378 SLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            5555 5889999999999999999999998665

>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=97.38  E-value=0.0018  Score=39.66  Aligned_cols=76  Identities=13%  Similarity=0.033  Sum_probs=63.7

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...|+...   +.+...|..+...+.+.|++++|...|+.... .. +.+...+..+-.++...|+++.|...|+..
T Consensus        26 ~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  103 (137)
T 3q49_B           26 PEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE-LD-GQSVKAHFFLGQCQLEMESYDEAIANLQRA  103 (137)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-hC-chhHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            46777777542   34678899999999999999999999999876 33 236778999999999999999999999988


Q ss_pred             h
Q 047113           79 V   79 (145)
Q Consensus        79 ~   79 (145)
                      .
T Consensus       104 ~  104 (137)
T 3q49_B          104 Y  104 (137)
T ss_dssp             H
T ss_pred             H
Confidence            8

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.36  E-value=0.0045  Score=34.86  Aligned_cols=79  Identities=19%  Similarity=0.196  Sum_probs=62.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCc-cHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~   93 (145)
                      +...|..+-..+.+.|++++|...|++... .. +.+...+..+-..+.+.|++++|...+++.. .  ..| +...+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~-~--~~p~~~~~~~~   82 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALE-LD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKAL-E--LDPNNAEAKQN   82 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHH-h--cCCCCHHHHHH
Confidence            456788899999999999999999999866 33 2367788889999999999999999999988 3  234 4555555


Q ss_pred             HHHHH
Q 047113           94 TVDLL   98 (145)
Q Consensus        94 li~~~   98 (145)
                      +..++
T Consensus        83 l~~~~   87 (91)
T 1na3_A           83 LGNAK   87 (91)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55444

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.35  E-value=0.00072  Score=51.74  Aligned_cols=97  Identities=10%  Similarity=-0.075  Sum_probs=73.2

Q ss_pred             HHHHcCChHHHHHHHHHhHhh--cCC---CCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHH
Q 047113           25 SHAIHGQEREALEAFYLVIHC--SDG---KPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLL   98 (145)
Q Consensus        25 a~~~~g~~~~A~~~~~~m~~~--~~~---~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~   98 (145)
                      .+...|++++|..++++....  .-+   .|+ ..+++.+..+|...|++++|+.++++...            .....|
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~------------i~~~~l  385 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVD------------GYMKLY  385 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH------------HHHHHS
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH------------HHHHHc
Confidence            355789999999999875321  222   233 45899999999999999999999998872            112233


Q ss_pred             hcCCCch-hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           99 ATGETEP-YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        99 ~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      +...|++ .+++.|-..|...|++++|+.++++..+
T Consensus       386 G~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~  421 (490)
T 3n71_A          386 HHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYA  421 (490)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3334554 5789999999999999999999998665

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.33  E-value=0.0038  Score=38.38  Aligned_cols=75  Identities=12%  Similarity=0.042  Sum_probs=62.7

Q ss_pred             chHHHHhccCCC--Cc----hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID--KN----VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~--~~----~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|.+.|+....  |+    ...|..+...+.+.|++++|...|+.... .  .| +...+..+-.++...|+++.|...
T Consensus        45 ~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~--~~~~~~~~~~~a~~~~~~~~~~~A~~~  121 (148)
T 2dba_A           45 GGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIE-K--DGGDVKALYRRSQALEKLGRLDQAVLD  121 (148)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--TSCCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHh-h--CccCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            467777775532  44    67899999999999999999999999866 3  34 677888889999999999999999


Q ss_pred             HHHhh
Q 047113           75 FDIMV   79 (145)
Q Consensus        75 ~~~m~   79 (145)
                      |++..
T Consensus       122 ~~~al  126 (148)
T 2dba_A          122 LQRCV  126 (148)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99988

>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=97.33  E-value=0.0016  Score=49.01  Aligned_cols=100  Identities=11%  Similarity=-0.069  Sum_probs=75.1

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhh--cCCCCc----HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           22 MIASHAIHGQEREALEAFYLVIHC--SDGKPN----NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~--~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .+..+.+.|++++|..++++....  .-+-|+    ..+++.+..+|...|++++|+.++++...-            .-
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i------------~~  360 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEP------------YR  360 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH------------HH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHh------------HH
Confidence            356677889999999999987531  223332    458899999999999999999999988721            11


Q ss_pred             HHHhcCCCch-hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           96 DLLATGETEP-YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        96 ~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..|+...|+. .+++.|-..|...|++++|+.++++..+
T Consensus       361 ~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          361 IFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            2223334444 5788899999999999999999998665

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.33  E-value=0.0011  Score=52.54  Aligned_cols=124  Identities=9%  Similarity=-0.035  Sum_probs=92.9

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+...   +.+...|..+-.++.+.|++++|...|++..+   +.| +...|..+-.++.+.|++++ ...|++
T Consensus       450 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~---l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~  525 (681)
T 2pzi_A          450 AKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDSATKHFTEVLD---TFPGELAPKLALAATAELAGNTDE-HKFYQT  525 (681)
T ss_dssp             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HSTTCSHHHHHHHHHHHHHTCCCT-TCHHHH
T ss_pred             HHHHHHHHHHhccCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHcCChHH-HHHHHH
Confidence            56777777653   34678899999999999999999999999866   345 57788899999999999999 999998


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC----------------CCc-hhhHHHHHHHHHhcc--------ChhHHHHHHccC
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG----------------ETE-PYVWGALLGACRIHH--------NVKIGELVAKDP  131 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~----------------~p~-~~~~~~li~~~~~~g--------~~~~a~~~~~~~  131 (145)
                      .. +  +.| +...|..+..+|.+.                .|+ ...|..+..++...|        ++++|.+.+..+
T Consensus       526 al-~--~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~  602 (681)
T 2pzi_A          526 VW-S--TNDGVISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEAL  602 (681)
T ss_dssp             HH-H--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTS
T ss_pred             HH-H--hCCchHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhC
Confidence            88 3  344 567788888877766                444 467777777776544        366666666555


Q ss_pred             C
Q 047113          132 F  132 (145)
Q Consensus       132 ~  132 (145)
                      .
T Consensus       603 ~  603 (681)
T 2pzi_A          603 P  603 (681)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.30  E-value=0.0034  Score=45.13  Aligned_cols=134  Identities=15%  Similarity=0.056  Sum_probs=100.0

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChH--HHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch------HHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQER--EALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL------IEE   70 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~--~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~------~~~   70 (145)
                      +++.++++.+   .++|-.+|+--.-...+.|+++  ++++.++.+.+ ...+ |-..|+.--....+.+.      +++
T Consensus       127 ~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~-~d~~-N~sAW~~R~~ll~~l~~~~~~~~~~e  204 (306)
T 3dra_A          127 YREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVID-TDLK-NNSAWSHRFFLLFSKKHLATDNTIDE  204 (306)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH-HCTT-CHHHHHHHHHHHHSSGGGCCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHH-hCCC-CHHHHHHHHHHHHhccccchhhhHHH
Confidence            3556666655   3457889998888889999998  99999999987 5533 77788877766777665      888


Q ss_pred             HHHHHHHhhhhcCcCccHHHHHHHHHHHhcC---------------------CCchhhHHHHHHHHHhccChhHHHHHHc
Q 047113           71 GIKVFDIMVHDFQLDLNLEHYGITVDLLATG---------------------ETEPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        71 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~---------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      +.+.++... ... .-|...|+.+--.+.+.                     ..+...+..+..+|.+.|+.++|.++++
T Consensus       205 El~~~~~aI-~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~  282 (306)
T 3dra_A          205 ELNYVKDKI-VKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYD  282 (306)
T ss_dssp             HHHHHHHHH-HHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHH-HhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Confidence            888888887 322 23677776555555443                     1255788889999999999999999999


Q ss_pred             cCCC-CCCCCC
Q 047113          130 DPFH-LDPKND  139 (145)
Q Consensus       130 ~~~~-~~~~~~  139 (145)
                      .+.+ .+|-..
T Consensus       283 ~l~~~~Dpir~  293 (306)
T 3dra_A          283 LLKSKYNPIRS  293 (306)
T ss_dssp             HHHHTTCGGGH
T ss_pred             HHHhccChHHH
Confidence            9885 777543

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.29  E-value=0.0029  Score=38.21  Aligned_cols=76  Identities=16%  Similarity=0.098  Sum_probs=61.0

Q ss_pred             chHHHHhccCCC--C-ch---hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHH
Q 047113            2 DDAERIFGGIID--K-NV---VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEG   71 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~~---~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a   71 (145)
                      ++|.+.|+....  | +.   ..|..+-.++.+.|++++|...|+.... ..  |+    ...+..+-.++.+.|+++.|
T Consensus        19 ~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~-~~--p~~~~~~~~~~~la~~~~~~g~~~~A   95 (129)
T 2xev_A           19 DDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVS-RY--PTHDKAAGGLLKLGLSQYGEGKNTEA   95 (129)
T ss_dssp             HHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC--TTSTTHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHH-HC--CCCcccHHHHHHHHHHHHHcCCHHHH
Confidence            467777776532  3 33   4788889999999999999999999876 32  43    56678888889999999999


Q ss_pred             HHHHHHhhh
Q 047113           72 IKVFDIMVH   80 (145)
Q Consensus        72 ~~~~~~m~~   80 (145)
                      ...|+....
T Consensus        96 ~~~~~~~~~  104 (129)
T 2xev_A           96 QQTLQQVAT  104 (129)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999983

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.25  E-value=0.0012  Score=47.61  Aligned_cols=118  Identities=8%  Similarity=-0.024  Sum_probs=66.7

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccch--------------------HHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGL--------------------IEEG   71 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~--------------------~~~a   71 (145)
                      ..+|..+...+...|++++|...|++......-.++    ..++..+-..+...|+                    ++.|
T Consensus        87 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A  166 (406)
T 3sf4_A           87 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAA  166 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHH
Confidence            446777777777778888777777765430110111    3366667777777777                    7777


Q ss_pred             HHHHHHhhhh---cCcCc-cHHHHHHHHHHHhcC-------------------CCc----hhhHHHHHHHHHhccChhHH
Q 047113           72 IKVFDIMVHD---FQLDL-NLEHYGITVDLLATG-------------------ETE----PYVWGALLGACRIHHNVKIG  124 (145)
Q Consensus        72 ~~~~~~m~~~---~~~~~-~~~~~~~li~~~~~~-------------------~p~----~~~~~~li~~~~~~g~~~~a  124 (145)
                      ...+......   .+-.| ...++..+...|...                   .++    ..++..+...|...|++++|
T Consensus       167 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  246 (406)
T 3sf4_A          167 VDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  246 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence            7777665421   11111 133444555444433                   111    22566666666677777777


Q ss_pred             HHHHccCCC
Q 047113          125 ELVAKDPFH  133 (145)
Q Consensus       125 ~~~~~~~~~  133 (145)
                      ...+++..+
T Consensus       247 ~~~~~~al~  255 (406)
T 3sf4_A          247 SEYYKKTLL  255 (406)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            766666544

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.23  E-value=0.00094  Score=48.57  Aligned_cols=118  Identities=6%  Similarity=-0.106  Sum_probs=70.2

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC-cHHHHHHHHHHhhccch-----------------HHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP-NNVTFLSILFACSYSGL-----------------IEEGIKV   74 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p-~~~~~~~ll~~~~~~~~-----------------~~~a~~~   74 (145)
                      ..+|..+-..|...|++++|...|++....   .+-.| ....+..+-..+...|+                 ++.|...
T Consensus       126 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~  205 (411)
T 4a1s_A          126 AKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEF  205 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHH
Confidence            456777778888888888888887775430   11122 34466777777777777                 7777777


Q ss_pred             HHHhhhh---cCcCc-cHHHHHHHHHHHhcC-------------------CCc----hhhHHHHHHHHHhccChhHHHHH
Q 047113           75 FDIMVHD---FQLDL-NLEHYGITVDLLATG-------------------ETE----PYVWGALLGACRIHHNVKIGELV  127 (145)
Q Consensus        75 ~~~m~~~---~~~~~-~~~~~~~li~~~~~~-------------------~p~----~~~~~~li~~~~~~g~~~~a~~~  127 (145)
                      +++....   .+-.+ ....+..+...|...                   .++    ..++..+...|...|++++|...
T Consensus       206 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  285 (411)
T 4a1s_A          206 YQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEH  285 (411)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            7665421   11111 233455555555544                   111    12566666777777777777777


Q ss_pred             HccCCC
Q 047113          128 AKDPFH  133 (145)
Q Consensus       128 ~~~~~~  133 (145)
                      +++..+
T Consensus       286 ~~~al~  291 (411)
T 4a1s_A          286 YKRTLA  291 (411)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766544

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.22  E-value=0.0019  Score=37.43  Aligned_cols=88  Identities=13%  Similarity=0.112  Sum_probs=63.9

Q ss_pred             HHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHH-HHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHh
Q 047113           22 MIASHAIHGQEREALEAFYLVIHCSDGKP-NNV-TFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA   99 (145)
Q Consensus        22 li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~   99 (145)
                      ....+.+.|++++|...|+...+ .  .| +.. .+..+-.++...|+++.|...|+... .  ..|+            
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~-~--~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~--~~p~------------   67 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQ-T--EPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAI-E--LNPD------------   67 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHH-H--CSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH-H--HCTT------------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH-H--CCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-h--cCCC------------
Confidence            44567889999999999999876 3  34 566 88888889999999999999999998 3  2332            


Q ss_pred             cCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113          100 TGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       100 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                          +...+..        +.+.++...+++.....|+++
T Consensus        68 ----~~~~~~~--------~~~~~a~~~~~~~~~~~p~~~   95 (99)
T 2kc7_A           68 ----SPALQAR--------KMVMDILNFYNKDMYNQLEHH   95 (99)
T ss_dssp             ----STHHHHH--------HHHHHHHHHHCCTTHHHHCCS
T ss_pred             ----cHHHHHH--------HHHHHHHHHHHHHhccCcccc
Confidence                1222211        567777777777776665444

>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=97.22  E-value=0.00025  Score=46.24  Aligned_cols=100  Identities=11%  Similarity=-0.003  Sum_probs=69.9

Q ss_pred             HHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchH----------HHHHHHHHHhhhhcCcCcc-HHHHHH
Q 047113           26 HAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLI----------EEGIKVFDIMVHDFQLDLN-LEHYGI   93 (145)
Q Consensus        26 ~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~----------~~a~~~~~~m~~~~~~~~~-~~~~~~   93 (145)
                      ..|.+++++|...++...+ .  .| +...|+.+-.++.+.+++          ++|...|++..   .+.|+ ...|..
T Consensus        12 ~~r~~~feeA~~~~~~Ai~-l--~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL---~ldP~~~~A~~~   85 (158)
T 1zu2_A           12 FDRILLFEQIRQDAENTYK-S--NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEAL---LIDPKKDEAVWC   85 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH---HHCTTCHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHH-H--CCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHH---HhCcCcHHHHHH
Confidence            3577789999999999866 3  45 677888888888887765          47888787777   35553 445555


Q ss_pred             HHHHHhcC---CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           94 TVDLLATG---ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        94 li~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      +..+|.+.   .|+..         ...|++++|...|++..+++|+++.
T Consensus        86 LG~ay~~lg~l~P~~~---------~a~g~~~eA~~~~~kAl~l~P~~~~  126 (158)
T 1zu2_A           86 IGNAYTSFAFLTPDET---------EAKHNFDLATQFFQQAVDEQPDNTH  126 (158)
T ss_dssp             HHHHHHHHHHHCCCHH---------HHHHHHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHhcccCcchh---------hhhccHHHHHHHHHHHHHhCCCCHH
Confidence            55544433   33331         1126999999999999999997654

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.21  E-value=0.0013  Score=45.77  Aligned_cols=118  Identities=8%  Similarity=-0.017  Sum_probs=69.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccch--------------------HHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGL--------------------IEEG   71 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~--------------------~~~a   71 (145)
                      ..+|..+...+...|++++|...|.+......-.++    ..++..+-..+...|+                    ++.|
T Consensus        83 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A  162 (338)
T 3ro2_A           83 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAA  162 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHH
Confidence            456777788888888888888888775431111112    3366777777777888                    7777


Q ss_pred             HHHHHHhhhh---cCcCc-cHHHHHHHHHHHhcC-------------------CC----chhhHHHHHHHHHhccChhHH
Q 047113           72 IKVFDIMVHD---FQLDL-NLEHYGITVDLLATG-------------------ET----EPYVWGALLGACRIHHNVKIG  124 (145)
Q Consensus        72 ~~~~~~m~~~---~~~~~-~~~~~~~li~~~~~~-------------------~p----~~~~~~~li~~~~~~g~~~~a  124 (145)
                      ...++.....   .+-.+ ....+..+...|...                   .+    ...++..+...+...|++++|
T Consensus       163 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  242 (338)
T 3ro2_A          163 VDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  242 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHH
Confidence            7777765421   11111 133444444444433                   11    122566666777777777777


Q ss_pred             HHHHccCCC
Q 047113          125 ELVAKDPFH  133 (145)
Q Consensus       125 ~~~~~~~~~  133 (145)
                      ...+++..+
T Consensus       243 ~~~~~~al~  251 (338)
T 3ro2_A          243 SEYYKKTLL  251 (338)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777766544

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.21  E-value=0.016  Score=40.57  Aligned_cols=112  Identities=9%  Similarity=-0.048  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCC---CCc--HHHHHHHHHHhhccchHHHHHHHHHHhhhh---cCcCc--cH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDG---KPN--NVTFLSILFACSYSGLIEEGIKVFDIMVHD---FQLDL--NL   88 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~---~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~--~~   88 (145)
                      +..+...+...|++++|+..|..... ...   .+.  ..+|+.+-..+...|+++.|...+++....   .+-.+  ..
T Consensus       118 ~~~~~~~~~~~~~~~~A~~~~~~al~-~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~  196 (293)
T 2qfc_A          118 QYYVAAYVLKKVDYEYCILELKKLLN-QQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDV  196 (293)
T ss_dssp             HHHHHHHHHTSSCHHHHHHHHHHHHT-TCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHH-HHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchH
Confidence            34455566677788888888877543 111   111  347777788888888888888888877621   11111  12


Q ss_pred             HHHHHHHHHHhcC----------------CC-------chhhHHHHHHHHHhccChhHH-HHHHccC
Q 047113           89 EHYGITVDLLATG----------------ET-------EPYVWGALLGACRIHHNVKIG-ELVAKDP  131 (145)
Q Consensus        89 ~~~~~li~~~~~~----------------~p-------~~~~~~~li~~~~~~g~~~~a-~~~~~~~  131 (145)
                      .+|..+..+|.+.                .+       -..+|..+-..|.+.|++++| ...+++.
T Consensus       197 ~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          197 KVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            4666666666655                11       145677777888888888888 6656543

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.21  E-value=0.0038  Score=47.74  Aligned_cols=105  Identities=9%  Similarity=-0.074  Sum_probs=78.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHh----hcC-CCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIH----CSD-GKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEH   90 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~----~~~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   90 (145)
                      .++|.|..+|...|++++|..++.+...    ..| -.|+ ..+++.|-..|...|++++|+.++++...          
T Consensus       352 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~----------  421 (490)
T 3n71_A          352 RLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYA----------  421 (490)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH----------
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH----------
Confidence            5899999999999999999999988532    022 2344 55899999999999999999999998772          


Q ss_pred             HHHHHHHHhcCCCch-hhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           91 YGITVDLLATGETEP-YVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        91 ~~~li~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                        .+-..++...|++ .+.+.+-.++...|.+++|+.++.++.+
T Consensus       422 --i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          422 --ILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             --HHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --HHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              1122233333433 3456666788888999999999988765

>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=97.18  E-value=0.004  Score=46.89  Aligned_cols=89  Identities=8%  Similarity=-0.028  Sum_probs=69.0

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ...|+.+-.++.+.|++++|+..|+...+ .. +.+...|..+-.++...|+++.|...|++.. .  +.|+        
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~-~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al-~--l~P~--------  383 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALG-LD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVL-E--VNPQ--------  383 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-T--TC----------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHh-cC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHH-H--hCCC--------
Confidence            57899999999999999999999999876 33 2368899999999999999999999999998 3  4443        


Q ss_pred             HHHhcCCCchhhHHHHHHHHHhccChhHHH
Q 047113           96 DLLATGETEPYVWGALLGACRIHHNVKIGE  125 (145)
Q Consensus        96 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~  125 (145)
                              +...+..+-..+.+.|+.+++.
T Consensus       384 --------~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          384 --------NKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHH
T ss_pred             --------CHHHHHHHHHHHHHHHHHHHHH
Confidence                    3445556666666666666554

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.13  E-value=0.02  Score=39.98  Aligned_cols=118  Identities=8%  Similarity=-0.036  Sum_probs=83.8

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcH----HHHHHHHHHhhccchHHHHHHHHHHhhhhc--CcCcc--H
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNN----VTFLSILFACSYSGLIEEGIKVFDIMVHDF--QLDLN--L   88 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~--~~~~~--~   88 (145)
                      ..+...+..+...|++++|.+.+..........++.    ..+..+...+...|+++.|...++......  ...+.  .
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            456677888999999999999998866512222211    233445566778899999999999876211  11222  4


Q ss_pred             HHHHHHHHHHhcC-------------------CCc-----hhhHHHHHHHHHhccChhHHHHHHccCCCC
Q 047113           89 EHYGITVDLLATG-------------------ETE-----PYVWGALLGACRIHHNVKIGELVAKDPFHL  134 (145)
Q Consensus        89 ~~~~~li~~~~~~-------------------~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  134 (145)
                      .+|+.+...|...                   .|+     ..+++.+...|...|++++|...+++..++
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~  225 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEI  225 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            5778888888766                   232     258889999999999999999999986653

>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=97.10  E-value=0.0025  Score=46.82  Aligned_cols=90  Identities=9%  Similarity=-0.014  Sum_probs=70.6

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      +...|+.+-.++.+.|++++|+..+++..+   +.| +...|..+-.++...|++++|...|++.. +  +.|+      
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~---~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al-~--l~P~------  339 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALE---IDPSNTKALYRRAQGWQGLKEYDQALADLKKAQ-E--IAPE------  339 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT------
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHH---hCchhHHHHHHHHHHHHHccCHHHHHHHHHHHH-H--hCCC------
Confidence            567899999999999999999999999865   345 67788999999999999999999999988 3  3343      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHH
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGEL  126 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  126 (145)
                                +...+..+-..+...++.+++.+
T Consensus       340 ----------~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          340 ----------DKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------CHHHHHHHHHHHHHHHHHHHHHH
Confidence                      34455555666666666666654

>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=97.07  E-value=0.0016  Score=42.33  Aligned_cols=92  Identities=13%  Similarity=0.031  Sum_probs=69.1

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCCh----------HHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc-
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQE----------REALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG-   66 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~----------~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~-   66 (145)
                      ++|.+.++..   .+.+...|+.+-.++.+.+++          ++|+..|++..+   +.| +...|..+-.++...| 
T Consensus        19 eeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~---ldP~~~~A~~~LG~ay~~lg~   95 (158)
T 1zu2_A           19 EQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL---IDPKKDEAVWCIGNAYTSFAF   95 (158)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHH---hCcCcHHHHHHHHHHHHHhcc
Confidence            5566666644   344778888888888888765          599999999866   456 5678888888998764 


Q ss_pred             ----------hHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHh
Q 047113           67 ----------LIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLA   99 (145)
Q Consensus        67 ----------~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~   99 (145)
                                ++++|...|++..   .+.|+-..|...+...-
T Consensus        96 l~P~~~~a~g~~~eA~~~~~kAl---~l~P~~~~y~~al~~~~  135 (158)
T 1zu2_A           96 LTPDETEAKHNFDLATQFFQQAV---DEQPDNTHYLKSLEMTA  135 (158)
T ss_dssp             HCCCHHHHHHHHHHHHHHHHHHH---HHCTTCHHHHHHHHHHH
T ss_pred             cCcchhhhhccHHHHHHHHHHHH---HhCCCCHHHHHHHHHHH
Confidence                      8999999999998   46777666665555443

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=97.05  E-value=0.016  Score=46.09  Aligned_cols=134  Identities=6%  Similarity=-0.071  Sum_probs=83.9

Q ss_pred             chHH-HHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCC---------CC------------cHHHHH
Q 047113            2 DDAE-RIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDG---------KP------------NNVTFL   56 (145)
Q Consensus         2 ~~A~-~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~---------~p------------~~~~~~   56 (145)
                      ++|. ++|+.-.   +++...|-..+...-+.|++++|..+|+.+.. ...         .|            ....|.
T Consensus       360 ~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~-~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi  438 (679)
T 4e6h_A          360 STVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCID-RIHLDLAALMEDDPTNESAINQLKSKLTYVYC  438 (679)
T ss_dssp             TTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-HHHHHhhhhhhccCcchhhhhhhccchHHHHH
Confidence            3454 6666432   23455677777778888888888888888765 210         13            133677


Q ss_pred             HHHHHhhccchHHHHHHHHHHhhhh-cCcCccHHHHHHHHHHHh-cC---------------CCchhhHHHHHHHHHhcc
Q 047113           57 SILFACSYSGLIEEGIKVFDIMVHD-FQLDLNLEHYGITVDLLA-TG---------------ETEPYVWGALLGACRIHH  119 (145)
Q Consensus        57 ~ll~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~~~~~~li~~~~-~~---------------~p~~~~~~~li~~~~~~g  119 (145)
                      ..+....+.|+.+.|..+|...... ....+.+....+.+.-.. +.               +.+...|...++-....|
T Consensus       439 ~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~  518 (679)
T 4e6h_A          439 VYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVN  518 (679)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCC
Confidence            7777778888888888888888732 122223333333333221 11               445566777777777788


Q ss_pred             ChhHHHHHHccCCCCCC
Q 047113          120 NVKIGELVAKDPFHLDP  136 (145)
Q Consensus       120 ~~~~a~~~~~~~~~~~~  136 (145)
                      +.+.|+.+|++.....|
T Consensus       519 ~~~~AR~lferal~~~~  535 (679)
T 4e6h_A          519 EESQVKSLFESSIDKIS  535 (679)
T ss_dssp             CHHHHHHHHHHHTTTSS
T ss_pred             CHHHHHHHHHHHHHhcC
Confidence            88888888888666444

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.02  E-value=0.0024  Score=37.49  Aligned_cols=70  Identities=9%  Similarity=0.011  Sum_probs=56.6

Q ss_pred             CcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHc
Q 047113           50 PNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAK  129 (145)
Q Consensus        50 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  129 (145)
                      ++...+..+-..+...|++++|...|+... .  ..|+                +...|..+-.++...|++++|...++
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al-~--~~p~----------------~~~~~~~lg~~~~~~g~~~~A~~~~~   62 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLI-T--AQPQ----------------NPVGYSNKAMALIKLGEYTQAIQMCQ   62 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHH-H--HCTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHH-h--cCCC----------------CHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            356678888889999999999999999988 3  2332                45667777888889999999999999


Q ss_pred             cCCCCCCCC
Q 047113          130 DPFHLDPKN  138 (145)
Q Consensus       130 ~~~~~~~~~  138 (145)
                      +..+..|++
T Consensus        63 ~al~~~p~~   71 (111)
T 2l6j_A           63 QGLRYTSTA   71 (111)
T ss_dssp             HHHTSCSST
T ss_pred             HHHHhCCCc
Confidence            988888865

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.97  E-value=0.0046  Score=39.29  Aligned_cols=63  Identities=16%  Similarity=0.161  Sum_probs=55.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +...|..+-.+|.+.|++++|+..++.... .. +.+...|..+-.++...|+++.|...|+...
T Consensus        62 ~~~~~~nla~~~~~~~~~~~A~~~~~~al~-~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al  124 (162)
T 3rkv_A           62 NIPLYANMSQCYLNIGDLHEAEETSSEVLK-RE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLL  124 (162)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHHHHHh-cC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHH
Confidence            346899999999999999999999999876 33 2367899999999999999999999999988

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.96  E-value=0.0011  Score=39.78  Aligned_cols=82  Identities=7%  Similarity=0.014  Sum_probs=60.1

Q ss_pred             HHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHH
Q 047113           33 REALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGAL  111 (145)
Q Consensus        33 ~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~l  111 (145)
                      ++|...|++..+   ..| +...+..+-..+...|+++.|...++... .  ..|+                +...|..+
T Consensus         2 ~~a~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--~~p~----------------~~~~~~~l   59 (115)
T 2kat_A            2 QAITERLEAMLA---QGTDNMLLRFTLGKTYAEHEQFDAALPHLRAAL-D--FDPT----------------YSVAWKWL   59 (115)
T ss_dssp             CCHHHHHHHHHT---TTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT----------------CHHHHHHH
T ss_pred             hHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHH-H--HCCC----------------cHHHHHHH
Confidence            356777877654   334 67788999999999999999999999988 3  2332                44556666


Q ss_pred             HHHHHhccChhHHHHHHccCCCCCC
Q 047113          112 LGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus       112 i~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      -..|...|++++|...+++..+..|
T Consensus        60 a~~~~~~g~~~~A~~~~~~al~~~~   84 (115)
T 2kat_A           60 GKTLQGQGDRAGARQAWESGLAAAQ   84 (115)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhcc
Confidence            7777778888888888777655443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=96.95  E-value=0.0048  Score=40.14  Aligned_cols=133  Identities=9%  Similarity=-0.056  Sum_probs=86.6

Q ss_pred             hHHHHhccCCCC--chhhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC--cHHHHHHHHHHhhccchHHHHHHHH
Q 047113            3 DAERIFGGIIDK--NVVIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP--NNVTFLSILFACSYSGLIEEGIKVF   75 (145)
Q Consensus         3 ~A~~~f~~m~~~--~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~   75 (145)
                      +|.++++....+  ...+++.+-..+...|++++|...|++....   .+-.|  ....+..+-..+...|++++|...+
T Consensus        51 ~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~  130 (203)
T 3gw4_A           51 ALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEY  130 (203)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            344444444332  3567999999999999999999999986541   12122  2346788888899999999999999


Q ss_pred             HHhhhhcCc--Cc--cHHHHHHHHHHHhcC-CC--chhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           76 DIMVHDFQL--DL--NLEHYGITVDLLATG-ET--EPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        76 ~~m~~~~~~--~~--~~~~~~~li~~~~~~-~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      ++......-  .+  -..++..+..+|.+. .+  -...+...+..+.+.|+....-.+...+....
T Consensus       131 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~  197 (203)
T 3gw4_A          131 EKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDIFAELEDSEAVNELMTRLNGLE  197 (203)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHhcccchh
Confidence            987622111  11  133355666666655 22  23467777777778887766656555555543

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=96.89  E-value=0.045  Score=41.11  Aligned_cols=60  Identities=7%  Similarity=-0.184  Sum_probs=26.3

Q ss_pred             hhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHHHHHHHhh
Q 047113           16 VVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGIKVFDIMV   79 (145)
Q Consensus        16 ~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~   79 (145)
                      ...+..|-..|..    .+++++|...|+...+ .|   +...+..+-..+..    .+++++|...|++..
T Consensus        75 ~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~-~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~  142 (490)
T 2xm6_A           75 TPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAAL-KG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAA  142 (490)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            3344444444444    4455555555544443 22   33333333333333    344444444444444

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=96.87  E-value=0.037  Score=41.56  Aligned_cols=90  Identities=8%  Similarity=-0.138  Sum_probs=45.7

Q ss_pred             hHHHHhccCCC-CchhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHHH
Q 047113            3 DAERIFGGIID-KNVVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGIK   73 (145)
Q Consensus         3 ~A~~~f~~m~~-~~~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~   73 (145)
                      +|.+.|+..-+ .+...+..|-..|..    .+++++|...|+...+ .|   +...+..+-..+..    .++++.|..
T Consensus        97 ~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~-~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~  172 (490)
T 2xm6_A           97 QAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAE-QG---RDSGQQSMGDAYFEGDGVTRDYVMARE  172 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            44444443322 244455555555555    5566666666666555 33   34444444444444    556666666


Q ss_pred             HHHHhhhhcCcCccHHHHHHHHHHHhc
Q 047113           74 VFDIMVHDFQLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        74 ~~~~m~~~~~~~~~~~~~~~li~~~~~  100 (145)
                      .|++.. +.|   +...+..|...|.+
T Consensus       173 ~~~~a~-~~~---~~~a~~~Lg~~y~~  195 (490)
T 2xm6_A          173 WYSKAA-EQG---NVWSCNQLGYMYSR  195 (490)
T ss_dssp             HHHHHH-HTT---CHHHHHHHHHHHHH
T ss_pred             HHHHHH-HCC---CHHHHHHHHHHHhc
Confidence            666655 322   34444444444443

>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=96.81  E-value=0.023  Score=36.33  Aligned_cols=76  Identities=5%  Similarity=0.094  Sum_probs=61.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHH-HHHcCCh--HHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIAS-HAIHGQE--REALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVF   75 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a-~~~~g~~--~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~   75 (145)
                      ++|.+.|+...   +.+...|..+..+ +.+.|++  ++|...|+.... .. +-+...+..+...+...|+++.|...+
T Consensus        61 ~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~la~~~~~~g~~~~A~~~~  138 (177)
T 2e2e_A           61 SNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRAMIDKALA-LD-SNEITALMLLASDAFMQANYAQAIELW  138 (177)
T ss_dssp             HHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHH-hC-CCcHHHHHHHHHHHHHcccHHHHHHHH
Confidence            46777777553   3467788888888 8899998  999999999876 33 225778888889999999999999999


Q ss_pred             HHhh
Q 047113           76 DIMV   79 (145)
Q Consensus        76 ~~m~   79 (145)
                      +...
T Consensus       139 ~~al  142 (177)
T 2e2e_A          139 QKVM  142 (177)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9988

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.80  E-value=0.001  Score=37.66  Aligned_cols=72  Identities=18%  Similarity=0.214  Sum_probs=57.6

Q ss_pred             cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           51 NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        51 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      +...+..+-..+...|+++.|...++... ..  .|+                +...|..+-..+...|++++|...+++
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~-~~--~~~----------------~~~~~~~l~~~~~~~~~~~~A~~~~~~   68 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKAL-EL--DPN----------------NAEAWYNLGNAYYKQGDYDEAIEYYQK   68 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHH-hc--CCC----------------CHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            45677788888999999999999999988 32  232                455677788889999999999999999


Q ss_pred             CCCCCCCCCCC
Q 047113          131 PFHLDPKNDAY  141 (145)
Q Consensus       131 ~~~~~~~~~~~  141 (145)
                      ..+..|+++..
T Consensus        69 a~~~~p~~~~~   79 (91)
T 1na3_A           69 ALELDPNNAEA   79 (91)
T ss_dssp             HHHHCTTCHHH
T ss_pred             HHhcCCCCHHH
Confidence            88888866543

>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=96.80  E-value=0.0085  Score=51.35  Aligned_cols=108  Identities=7%  Similarity=-0.105  Sum_probs=73.6

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      ++...|..+-..|...|++++|..+|...          ..|..+..++.+.|+++.|.+.+++..       +..+|..
T Consensus      1193 ~n~ad~~~iGd~le~eg~YeeA~~~Y~kA----------~ny~rLA~tLvkLge~q~AIEaarKA~-------n~~aWke 1255 (1630)
T 1xi4_A         1193 PNNAHIQQVGDRCYDEKMYDAAKLLYNNV----------SNFGRLASTLVHLGEYQAAVDGARKAN-------STRTWKE 1255 (1630)
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHhh----------hHHHHHHHHHHHhCCHHHHHHHHHHhC-------CHHHHHH
Confidence            45555666667777777777777777652          367777777777777777777776654       3455655


Q ss_pred             HHHHHhcC-------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           94 TVDLLATG-------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        94 li~~~~~~-------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      +-.+|...             ..+...+..++.-|.+.|.+++|.++++....+++..
T Consensus      1256 v~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~LeraH 1313 (1630)
T 1xi4_A         1256 VCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAH 1313 (1630)
T ss_pred             HHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccChhH
Confidence            54444322             3345566788899999999999999998877766543

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=96.80  E-value=0.034  Score=37.08  Aligned_cols=126  Identities=6%  Similarity=-0.142  Sum_probs=91.9

Q ss_pred             chHHHHhccCCC-CchhhHHHHHHHHHHcC----ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHH
Q 047113            2 DDAERIFGGIID-KNVVIWSGMIASHAIHG----QEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m~~-~~~~~~~~li~a~~~~g----~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~   72 (145)
                      ++|.+.|+..-. .+...+..|-..|.+ +    ++++|...|+...+ .|   +...+..+-..+..    .+++++|.
T Consensus        35 ~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~-~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~  109 (212)
T 3rjv_A           35 QKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVE-AG---SKSGEIVLARVLVNRQAGATDVAHAI  109 (212)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHTCGGGSSCCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHHcCCCCccCHHHHH
Confidence            467777775533 467778888888877 6    89999999999877 43   66677777777776    88999999


Q ss_pred             HHHHHhhhhcCcC-ccHHHHHHHHHHHhcC-------------------C-CchhhHHHHHHHHHhc-c-----ChhHHH
Q 047113           73 KVFDIMVHDFQLD-LNLEHYGITVDLLATG-------------------E-TEPYVWGALLGACRIH-H-----NVKIGE  125 (145)
Q Consensus        73 ~~~~~m~~~~~~~-~~~~~~~~li~~~~~~-------------------~-p~~~~~~~li~~~~~~-g-----~~~~a~  125 (145)
                      ..|++.. +.|-. .+...+..|-.+|...                   . .+...+..|-..|... |     ++++|.
T Consensus       110 ~~~~~A~-~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~  188 (212)
T 3rjv_A          110 TLLQDAA-RDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKAL  188 (212)
T ss_dssp             HHHHHHT-SSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHH
T ss_pred             HHHHHHH-HcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHH
Confidence            9999998 54432 1266777777777662                   3 5666777777777654 3     889999


Q ss_pred             HHHccCCC
Q 047113          126 LVAKDPFH  133 (145)
Q Consensus       126 ~~~~~~~~  133 (145)
                      ..+++..+
T Consensus       189 ~~~~~A~~  196 (212)
T 3rjv_A          189 HWLNVSCL  196 (212)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=96.71  E-value=0.067  Score=38.32  Aligned_cols=116  Identities=9%  Similarity=-0.036  Sum_probs=73.9

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCC--C--cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGK--P--NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~--p--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      ..+..+-..+...|++++|...+++... ..-.  +  ....+..+-..+...|++++|...++.......-......+.
T Consensus       136 ~~~~~la~~~~~~g~~~~A~~~~~~al~-~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~  214 (373)
T 1hz4_A          136 FLVRIRAQLLWAWARLDEAEASARSGIE-VLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWI  214 (373)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-HTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHH-HhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHH
Confidence            4677788899999999999999998654 2211  1  235677888889999999999999998872211111111121


Q ss_pred             H-----HHHHHhcC----------------CCc-----hhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           93 I-----TVDLLATG----------------ETE-----PYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        93 ~-----li~~~~~~----------------~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .     .+..+...                .|.     ...+..+...+...|++++|...+++...
T Consensus       215 ~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~  281 (373)
T 1hz4_A          215 SNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNE  281 (373)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1     11222222                111     12456666777788888888887776544

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.54  E-value=0.025  Score=41.28  Aligned_cols=116  Identities=7%  Similarity=-0.201  Sum_probs=79.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHH----HHHHHHHHhhccchHHHHHHHHHHhhhh---cCcCc-cHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNV----TFLSILFACSYSGLIEEGIKVFDIMVHD---FQLDL-NLE   89 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~----~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~-~~~   89 (145)
                      ++..|...|.+.|++++|.+.+.......+-.++..    ..+.+-..+...|+++.+..++......   .+..+ -..
T Consensus        57 al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  136 (434)
T 4b4t_Q           57 SILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHS  136 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHH
Confidence            478899999999999999999998754233233332    2233334445678889999888877631   22222 244


Q ss_pred             HHHHHHHHHhcC----------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           90 HYGITVDLLATG----------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        90 ~~~~li~~~~~~----------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ++..|...|...                      .+ ...++..++..|...|++++|..++++...
T Consensus       137 ~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  203 (434)
T 4b4t_Q          137 LSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAART  203 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHH
Confidence            555666665544                      22 235899999999999999999999887655

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=96.54  E-value=0.01  Score=47.18  Aligned_cols=119  Identities=9%  Similarity=-0.037  Sum_probs=85.5

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhc-C-CCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCS-D-GKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~-~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ..|-..+....+.|..+.|..+|....+ . + ..+......+.+.-.. .++.+.|..+|+...+.  +.-+...|...
T Consensus       435 ~vWi~y~~~erR~~~l~~AR~vf~~A~~-~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~--~p~~~~~w~~y  510 (679)
T 4e6h_A          435 YVYCVYMNTMKRIQGLAASRKIFGKCRR-LKKLVTPDIYLENAYIEYHI-SKDTKTACKVLELGLKY--FATDGEYINKY  510 (679)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHH-TGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHHHH--HTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH-hcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHH--CCCchHHHHHH
Confidence            3688889988999999999999999877 4 2 2233334444444332 35689999999999843  33355566666


Q ss_pred             HHHHhcC----------------CC----chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           95 VDLLATG----------------ET----EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        95 i~~~~~~----------------~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ++.....                .|    ....|...+.-=...|+.+.+..+.+++.+..|+++
T Consensus       511 ~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~  575 (679)
T 4e6h_A          511 LDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVN  575 (679)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCC
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCc
Confidence            6544322                33    235788888888889999999999999999888655

>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=96.51  E-value=0.019  Score=40.58  Aligned_cols=120  Identities=6%  Similarity=-0.104  Sum_probs=86.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhh---cCcCc-cH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHD---FQLDL-NL   88 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~-~~   88 (145)
                      ..|+.....|...|++++|...|......   .+-.+. ..+|+.+...+.+.|++++|...+++...-   .|-.. -.
T Consensus        37 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a  116 (307)
T 2ifu_A           37 SEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAA  116 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            36888889999999999999999886441   121111 458888999999999999999999877621   12111 24


Q ss_pred             HHHHHHHHHHhcC---------------CC-------chhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           89 EHYGITVDLLATG---------------ET-------EPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        89 ~~~~~li~~~~~~---------------~p-------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .++..+..+|.+.               .|       ...+++.+-..|.+.|++++|...+++..++.|
T Consensus       117 ~~~~~lg~~~~~g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~  186 (307)
T 2ifu_A          117 MALDRAGKLMEPLDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYK  186 (307)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            5666666666432               11       145788889999999999999999998776443

>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=96.51  E-value=0.0048  Score=40.18  Aligned_cols=72  Identities=18%  Similarity=0.071  Sum_probs=58.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhc-----CCCCc-HHHH----HHHHHHhhccchHHHHHHHHHHhhh----hcC
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCS-----DGKPN-NVTF----LSILFACSYSGLIEEGIKVFDIMVH----DFQ   83 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~-----~~~p~-~~~~----~~ll~~~~~~~~~~~a~~~~~~m~~----~~~   83 (145)
                      .|+.+-.++.+.|++++|+..|+...+ .     .+.|+ ...|    ...-.++...|++++|...|++...    +.|
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~-l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~  137 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALH-YFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKG  137 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH-hhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHH
Confidence            899999999999999999999999876 3     22675 5688    8888999999999999999998873    345


Q ss_pred             cCccHHH
Q 047113           84 LDLNLEH   90 (145)
Q Consensus        84 ~~~~~~~   90 (145)
                      +.+....
T Consensus       138 ~~~~~~~  144 (159)
T 2hr2_A          138 ETPGKER  144 (159)
T ss_dssp             CCTTHHH
T ss_pred             HHHHHHH
Confidence            5544333

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.50  E-value=0.053  Score=40.60  Aligned_cols=121  Identities=12%  Similarity=0.028  Sum_probs=79.7

Q ss_pred             HHHHhccCCCCchhhHHHHHHHHHHcC---ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhcc----chHHHHHHHHH
Q 047113            4 AERIFGGIIDKNVVIWSGMIASHAIHG---QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYS----GLIEEGIKVFD   76 (145)
Q Consensus         4 A~~~f~~m~~~~~~~~~~li~a~~~~g---~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~----~~~~~a~~~~~   76 (145)
                      |..++......+...+..|-..|.+.|   +.++|...|+...+ .| .++...+..+-..+...    +++++|...|+
T Consensus       164 a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~-~g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~  241 (452)
T 3e4b_A          164 VERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVS-RG-TVTAQRVDSVARVLGDATLGTPDEKTAQALLE  241 (452)
T ss_dssp             HHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-TT-CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHH-CC-CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence            444555555556668888888999999   89999999998877 66 34555444555555444    68888888888


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHh----cC--------------CCchhhHHHHHHHHHhcc-----ChhHHHHHHccCC
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLA----TG--------------ETEPYVWGALLGACRIHH-----NVKIGELVAKDPF  132 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~----~~--------------~p~~~~~~~li~~~~~~g-----~~~~a~~~~~~~~  132 (145)
                      ...     .-+...+..|..+|.    ..              ..+...+..|-..|. .|     ++++|...|++..
T Consensus       242 ~aa-----~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa  314 (452)
T 3e4b_A          242 KIA-----PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV  314 (452)
T ss_dssp             HHG-----GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT
T ss_pred             HHc-----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh
Confidence            875     223445555555522    11              335556666666665 55     8888888888765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=96.47  E-value=0.062  Score=38.48  Aligned_cols=116  Identities=8%  Similarity=-0.056  Sum_probs=80.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcC--c-c
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN----NVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLD--L-N   87 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~--~-~   87 (145)
                      .++.+-..+...|++++|...+++......-.++    ..+++.+-..+...|+++.|...++......   +..  | .
T Consensus        55 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~  134 (373)
T 1hz4_A           55 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMH  134 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHH
Confidence            5777778889999999999999886431111112    2335667778889999999999998877321   222  3 2


Q ss_pred             HHHHHHHHHHHhcC----------------CC------chhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           88 LEHYGITVDLLATG----------------ET------EPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        88 ~~~~~~li~~~~~~----------------~p------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ...+..+...|...                .+      ...++..+-..+...|++++|...+++..+
T Consensus       135 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~  202 (373)
T 1hz4_A          135 EFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLEN  202 (373)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34555566666544                11      234677888889999999999999988765

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.37  E-value=0.038  Score=39.27  Aligned_cols=90  Identities=8%  Similarity=-0.113  Sum_probs=66.4

Q ss_pred             chHHHHhccCCC-Cc----hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc--HHHHHHHHHHhhccchHHHHHHH
Q 047113            2 DDAERIFGGIID-KN----VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN--NVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus         2 ~~A~~~f~~m~~-~~----~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      ++|++.|+.... ++    ...+..+-.++.+.|++++|+..|++... ....|.  .......-.++.+.|+.++|..+
T Consensus       152 ~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~-g~~~P~~~~da~~~~glaL~~lGr~deA~~~  230 (282)
T 4f3v_A          152 TDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALFTEAERRLTEAND-SPAGEACARAIAWYLAMARRSQGNESAAVAL  230 (282)
T ss_dssp             HHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-STTTTTTHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhc-CCCCccccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            567888876543 22    23688889999999999999999999865 443253  33556666778999999999999


Q ss_pred             HHHhhhhcCcCccHHHHHHHH
Q 047113           75 FDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        75 ~~~m~~~~~~~~~~~~~~~li   95 (145)
                      |+++. .  ..|+...+..|.
T Consensus       231 l~~a~-a--~~P~~~~~~aL~  248 (282)
T 4f3v_A          231 LEWLQ-T--THPEPKVAAALK  248 (282)
T ss_dssp             HHHHH-H--HSCCHHHHHHHH
T ss_pred             HHHHH-h--cCCcHHHHHHHh
Confidence            99998 3  355555555554

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.34  E-value=0.015  Score=34.00  Aligned_cols=65  Identities=8%  Similarity=-0.045  Sum_probs=49.4

Q ss_pred             cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           51 NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        51 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      +...+..+-..+.+.|++++|...|++.. +  ..|+                +...|..+-.+|...|++++|...+++
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--~~p~----------------~~~a~~~lg~~~~~~g~~~~A~~~~~~   66 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELV-E--TDPD----------------YVGTYYHLGKLYERLDRTDDAIDTYAQ   66 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HSTT----------------CTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCCC----------------cHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            56788888899999999999999999998 3  2332                445666677777777788777777776


Q ss_pred             CCCC
Q 047113          131 PFHL  134 (145)
Q Consensus       131 ~~~~  134 (145)
                      ..++
T Consensus        67 al~l   70 (100)
T 3ma5_A           67 GIEV   70 (100)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            5543

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.23  E-value=0.032  Score=40.70  Aligned_cols=109  Identities=8%  Similarity=-0.057  Sum_probs=73.8

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCC-Cc---------------HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGK-PN---------------NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN   87 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~-p~---------------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~   87 (145)
                      ..+.+.|++++|.+.|....+ ..-. .+               ...+..+...|.+.|+++++.+.+.......+-.++
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLD-KDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHH-SCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHh-hCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            346789999999999999865 2211 11               124778899999999999999999887732222222


Q ss_pred             HH---HHHHHHHHHhcC-----------------------CCc-hhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           88 LE---HYGITVDLLATG-----------------------ETE-PYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        88 ~~---~~~~li~~~~~~-----------------------~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..   .....+..+...                       .+. ..++..+...|...|++++|..+++.+..
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~  163 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLR  163 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHH
Confidence            21   122222222221                       222 35788899999999999999999988655

>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=96.18  E-value=0.027  Score=42.40  Aligned_cols=63  Identities=11%  Similarity=-0.091  Sum_probs=52.8

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHh----hcC-CCCc-HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIH----CSD-GKPN-NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~----~~~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .++|.|..+|...|++++|..++++...    ..| -.|+ ..+++.+-..|...|++++|+.++++..
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            5899999999999999999999998632    022 3444 4589999999999999999999999877

>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=96.17  E-value=0.021  Score=44.33  Aligned_cols=132  Identities=11%  Similarity=0.059  Sum_probs=87.4

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcC--ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc-hHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHG--QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSG-LIEEGIKVF   75 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g--~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~-~~~~a~~~~   75 (145)
                      ++|.+.++.+-   +++-.+|+---.++.+.|  +++++++.++.+.+ ... -|...|+.---...+.| .++++.+.+
T Consensus        90 ~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~-~d~-~N~~aW~~R~~~l~~l~~~~~~el~~~  167 (567)
T 1dce_A           90 KAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLE-ADE-RNFHCWDYRRFVAAQAAVAPAEELAFT  167 (567)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHH-HCT-TCHHHHHHHHHHHHHTCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHh-hcc-ccccHHHHHHHHHHHcCCChHHHHHHH
Confidence            35666666552   346778988888888889  67999999999987 542 37778888887888888 788888888


Q ss_pred             HHhhhhcCcCc-cHHHHHHHHHHHhcCCCc--hhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCcc
Q 047113           76 DIMVHDFQLDL-NLEHYGITVDLLATGETE--PYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYYT  143 (145)
Q Consensus        76 ~~m~~~~~~~~-~~~~~~~li~~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  143 (145)
                      +.+. +.  .| |...|+....++.+..+.  ....     +-...+.++++.+.+++..+..|++.+.|.
T Consensus       168 ~~~I-~~--~p~n~saW~~r~~ll~~l~~~~~~~~~-----~~~~~~~~~eel~~~~~ai~~~P~~~saW~  230 (567)
T 1dce_A          168 DSLI-TR--NFSNYSSWHYRSCLLPQLHPQPDSGPQ-----GRLPENVLLKELELVQNAFFTDPNDQSAWF  230 (567)
T ss_dssp             HTTT-TT--TCCCHHHHHHHHHHHHHHSCCCCSSSC-----CSSCHHHHHHHHHHHHHHHHHCSSCSHHHH
T ss_pred             HHHH-HH--CCCCccHHHHHHHHHHhhccccccccc-----ccccHHHHHHHHHHHHHHHhhCCCCccHHH
Confidence            8888 33  33 444444444333221000  0000     000126679999999998888998876553

>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=96.12  E-value=0.059  Score=41.85  Aligned_cols=119  Identities=7%  Similarity=-0.028  Sum_probs=89.5

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCC----------hHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc--h
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQ----------EREALEAFYLVIHCSDGKPNNVTFLSILFACSYSG--L   67 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~----------~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~--~   67 (145)
                      +|.+.++.+-   +.+...|+.--.++.+.|+          ++++++.++.+.+ ..- -+...|+.---...+.+  +
T Consensus        47 eal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~-~~p-K~y~aW~hR~w~l~~l~~~~  124 (567)
T 1dce_A           47 SVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLR-VNP-KSYGTWHHRCWLLSRLPEPN  124 (567)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH-HCT-TCHHHHHHHHHHHHTCSSCC
T ss_pred             HHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHH-hCC-CCHHHHHHHHHHHHHccccc
Confidence            4555555442   2355678877777777777          9999999999876 442 26778888888888888  7


Q ss_pred             HHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhcc-ChhHHHHHHccCCCCCCCCCCCc
Q 047113           68 IEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHH-NVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        68 ~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      ++++.+.++++. +  ..|                .+..+|+.--.+..+.| .++++++.++++.+.+|.+.++|
T Consensus       125 ~~~el~~~~k~l-~--~d~----------------~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW  181 (567)
T 1dce_A          125 WARELELCARFL-E--ADE----------------RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSW  181 (567)
T ss_dssp             HHHHHHHHHHHH-H--HCT----------------TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHH
T ss_pred             HHHHHHHHHHHH-h--hcc----------------ccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHH
Confidence            799999999998 3  233                36677777777777888 88999999999999888776554

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.01  E-value=0.0055  Score=35.38  Aligned_cols=65  Identities=12%  Similarity=0.090  Sum_probs=51.2

Q ss_pred             HHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchh-hHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           59 LFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPY-VWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        59 l~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      ...+.+.|+++.|...++... .  ..|+                +.. .|..+-.+|...|++++|...|++..+..|+
T Consensus         7 a~~~~~~~~~~~A~~~~~~al-~--~~p~----------------~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~   67 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFL-Q--TEPV----------------GKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPD   67 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHH-H--HCSS----------------THHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHcCCHHHHHHHHHHHH-H--HCCC----------------cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence            345678899999999999988 3  2332                445 6777788899999999999999999998887


Q ss_pred             CCCCc
Q 047113          138 NDAYY  142 (145)
Q Consensus       138 ~~~~~  142 (145)
                      ++..+
T Consensus        68 ~~~~~   72 (99)
T 2kc7_A           68 SPALQ   72 (99)
T ss_dssp             STHHH
T ss_pred             cHHHH
Confidence            76543

>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=95.75  E-value=0.043  Score=32.90  Aligned_cols=64  Identities=13%  Similarity=0.162  Sum_probs=51.3

Q ss_pred             ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           31 QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        31 ~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      |.=+..+-++.+-. .++.|+.....+.+.+|.+-+++..|.++|+-++.+.|  +...+|..+++-
T Consensus        25 D~~e~rrglN~l~~-~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~--~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVG-YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTT-SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CchhhHHHHHHH
Confidence            34467777777777 88999999999999999999999999999999984443  335567777653

>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=95.65  E-value=0.19  Score=31.08  Aligned_cols=105  Identities=4%  Similarity=-0.128  Sum_probs=63.0

Q ss_pred             chHHHHhccCCC-CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHHHHHH
Q 047113            2 DDAERIFGGIID-KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~-~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~   76 (145)
                      ++|.+.|+..-+ .+....  |-..|...+.+++|.+.|+...+ .   -+...+..+-..+..    .+++++|...|+
T Consensus        12 ~~A~~~~~~aa~~g~~~a~--lg~~y~~g~~~~~A~~~~~~Aa~-~---g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~   85 (138)
T 1klx_A           12 KKAIQYYVKACELNEMFGC--LSLVSNSQINKQKLFQYLSKACE-L---NSGNGCRFLGDFYENGKYVKKDLRKAAQYYS   85 (138)
T ss_dssp             HHHHHHHHHHHHTTCTTHH--HHHHTCTTSCHHHHHHHHHHHHH-T---TCHHHHHHHHHHHHHCSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHhhh--HHHHHHcCCCHHHHHHHHHHHHc-C---CCHHHHHHHHHHHHcCCCCCccHHHHHHHHH
Confidence            356666664432 233333  55555566677778888887766 4   355666666666665    678888888888


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHh----ccChhHHHHHHccCCC
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRI----HHNVKIGELVAKDPFH  133 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~  133 (145)
                      +.. +.|                    +...+..|-..|..    .+++++|...+++..+
T Consensus        86 ~Aa-~~g--------------------~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~  125 (138)
T 1klx_A           86 KAC-GLN--------------------DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACR  125 (138)
T ss_dssp             HHH-HTT--------------------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             HHH-cCC--------------------CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHH
Confidence            877 444                    22333344444444    5667777777665444

>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=95.55  E-value=0.084  Score=38.96  Aligned_cols=73  Identities=12%  Similarity=0.128  Sum_probs=60.9

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      .+..+|..+-..+...|++++|...+++... .+  |+...|..+-..+.-.|++++|.+.+++..   .+.|...||.
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~-Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Al---rL~P~~~t~~  347 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGID-LE--MSWLNYVLLGKVYEMKGMNREAADAYLTAF---NLRPGANTLY  347 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHH---HHSCSHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHh-cC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHH---hcCCCcChHH
Confidence            4677888887777888999999999999988 55  888888888888899999999999999887   3566666554

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=95.39  E-value=0.084  Score=32.22  Aligned_cols=85  Identities=8%  Similarity=-0.049  Sum_probs=58.6

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhh---cCcCc-cH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHD---FQLDL-NL   88 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~-~~   88 (145)
                      .++..+-..+...|++++|...|++....   .+-.+ ....+..+-..+...|++++|...+++....   .+-.+ ..
T Consensus        50 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  129 (164)
T 3ro3_A           50 IAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEG  129 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHH
Confidence            47889999999999999999999986431   11111 1456778888899999999999999887732   12111 23


Q ss_pred             HHHHHHHHHHhcC
Q 047113           89 EHYGITVDLLATG  101 (145)
Q Consensus        89 ~~~~~li~~~~~~  101 (145)
                      ..+..+...|...
T Consensus       130 ~~~~~la~~~~~~  142 (164)
T 3ro3_A          130 RACWSLGNAYTAL  142 (164)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            4455555555443

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.34  E-value=0.087  Score=30.70  Aligned_cols=63  Identities=11%  Similarity=0.037  Sum_probs=44.3

Q ss_pred             CchhhHHHHHHHHHHcCC---hHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           14 KNVVIWSGMIASHAIHGQ---EREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~---~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +|...|..+-.++...++   .++|..+|++...   +.| +......+-..+.+.|++++|...|+.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~---~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l   70 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQ---LEPYNEAALSLIANDHFISFRFQEAIDTWVLLL   70 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH---HCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            355666666666665544   6788888887765   345 45666777777788888888888888877

>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=95.26  E-value=0.054  Score=40.65  Aligned_cols=63  Identities=13%  Similarity=0.062  Sum_probs=52.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHh----hcC-CCCc-HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIH----CSD-GKPN-NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~----~~~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .+++.|..+|...|++++|+.++.+...    ..| -.|+ ..+++.+-..+...|++++|+.++++..
T Consensus       330 ~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          330 KVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            5899999999999999999999997632    022 3444 4588999999999999999999998776

>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=95.22  E-value=0.1  Score=37.86  Aligned_cols=133  Identities=13%  Similarity=0.088  Sum_probs=85.0

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcC--ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch-HHHHHHHHH
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHG--QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL-IEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g--~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~-~~~a~~~~~   76 (145)
                      ++.++++.+-   +++..+|+---..+.+.|  ++++++.+++.+.+ .. +-|-..|+.---.....|. ++.+.+.+.
T Consensus        92 ~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~-~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~  169 (331)
T 3dss_A           92 AELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLE-AD-ERNFHCWDYRRFVAAQAAVAPAEELAFTD  169 (331)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHH
Confidence            4555565442   357778988888888888  48999999999977 44 2377788887777777787 588888888


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      .+. ... ..|...|+.....+.+..++... .  -.+-...+.++++++.+.......|++.+.+
T Consensus       170 ~~I-~~~-p~N~SAW~~R~~ll~~l~~~~~~-~--~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW  230 (331)
T 3dss_A          170 SLI-TRN-FSNYSSWHYRSCLLPQLHPQPDS-G--PQGRLPENVLLKELELVQNAFFTDPNDQSAW  230 (331)
T ss_dssp             HHH-HHC-SCCHHHHHHHHHHHHHHSCCC---------CCCHHHHHHHHHHHHHHHHHSTTCHHHH
T ss_pred             HHH-HHC-CCCHHHHHHHHHHHHHhhhcccc-c--cccccchHHHHHHHHHHHHHHHhCCCCHHHH
Confidence            888 433 22445555444333222111000 0  0000011568899999999888999887655

>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=95.12  E-value=0.48  Score=34.64  Aligned_cols=129  Identities=13%  Similarity=0.054  Sum_probs=85.2

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCChH--------HHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch----
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQER--------EALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL----   67 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~--------~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~----   67 (145)
                      ++.++++.+-   ++|-..|+--.-...+.|+++        ++++.++.+.+ ... -|...|+..-....+.+.    
T Consensus       143 ~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~-~dp-~N~SAW~~R~~lL~~l~~~~~~  220 (349)
T 3q7a_A          143 SEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLR-VDG-RNNSAWGWRWYLRVSRPGAETS  220 (349)
T ss_dssp             HHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHH-HCT-TCHHHHHHHHHHHTTSTTCCCC
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHH-hCC-CCHHHHHHHHHHHHhccccccc
Confidence            4556666543   346777877666666666666        88888888876 442 277778777777776664    


Q ss_pred             ---HHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcC------------------------------------------
Q 047113           68 ---IEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATG------------------------------------------  101 (145)
Q Consensus        68 ---~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~------------------------------------------  101 (145)
                         ++++.+.++... .  ..| |...|+.+--.+.+.                                          
T Consensus       221 ~~~~~eELe~~~~aI-~--~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  297 (349)
T 3q7a_A          221 SRSLQDELIYILKSI-H--LIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDT  297 (349)
T ss_dssp             HHHHHHHHHHHHHHH-H--HCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSC
T ss_pred             hHHHHHHHHHHHHHH-H--hCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhccccccc
Confidence               566777776666 2  333 566665433322211                                          


Q ss_pred             -CCchhhHHHHHHHHHhccChhHHHHHHccCC-CCCC
Q 047113          102 -ETEPYVWGALLGACRIHHNVKIGELVAKDPF-HLDP  136 (145)
Q Consensus       102 -~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~  136 (145)
                       .+....+..|.+.|...|+.++|.++++.+. +.+|
T Consensus       298 ~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~~dp  334 (349)
T 3q7a_A          298 PLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEYDQ  334 (349)
T ss_dssp             CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCG
T ss_pred             CCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhhCh
Confidence             1455677888889999999999999999875 4555

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.10  E-value=0.19  Score=39.77  Aligned_cols=47  Identities=13%  Similarity=-0.072  Sum_probs=31.1

Q ss_pred             HHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           26 HAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        26 ~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ..+.|++++|.++.+.+       .+...|..+-..|.+.++++.|++.|..+.
T Consensus       662 ~l~~~~~~~A~~~~~~~-------~~~~~W~~la~~al~~~~~~~A~~~y~~~~  708 (814)
T 3mkq_A          662 ALKVGQLTLARDLLTDE-------SAEMKWRALGDASLQRFNFKLAIEAFTNAH  708 (814)
T ss_dssp             HHHHTCHHHHHHHHTTC-------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             hhhcCCHHHHHHHHHhh-------CcHhHHHHHHHHHHHcCCHHHHHHHHHHcc
Confidence            45567777777665433       245667777777777777777777777665

>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=95.07  E-value=0.2  Score=36.37  Aligned_cols=126  Identities=12%  Similarity=0.027  Sum_probs=80.0

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCC-hHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhcc------------
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQ-EREALEAFYLVIHCSDGKPNNVTFLSILFACSYS------------   65 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~-~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~------------   65 (145)
                      +++.++++.+   .++|-+.|+--.-...+.|+ ++++++.++.+.+ ... -|...|+..-......            
T Consensus       127 ~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~-~~p-~N~SAW~~R~~ll~~l~~~~~~~~~~~~  204 (331)
T 3dss_A          127 ARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLIT-RNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRL  204 (331)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-HCS-CCHHHHHHHHHHHHHHSCCC------CC
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHH-HCC-CCHHHHHHHHHHHHHhhhcccccccccc
Confidence            3566666655   34688899988888889998 5999999999987 553 3777887766665544            


Q ss_pred             --chHHHHHHHHHHhhhhcCcCc-cHHHHHHHHHHHhcCCC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           66 --GLIEEGIKVFDIMVHDFQLDL-NLEHYGITVDLLATGET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        66 --~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                        +.++++.+.+.... .  ..| |...|+-+--.+.+... ...+       -.+.+.++++++.++++.+.+|++.
T Consensus       205 ~~~~~~eEle~~~~ai-~--~~P~d~SaW~Y~r~ll~~~~~~~~~~-------~~~~~~l~~el~~~~elle~~pd~~  272 (331)
T 3dss_A          205 PENVLLKELELVQNAF-F--TDPNDQSAWFYHRWLLGAGSGRCELS-------VEKSTVLQSELESCKELQELEPENK  272 (331)
T ss_dssp             CHHHHHHHHHHHHHHH-H--HSTTCHHHHHHHHHHHHSSSCGGGCC-------HHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             chHHHHHHHHHHHHHH-H--hCCCCHHHHHHHHHHHHhccCccccc-------hHHHHHHHHHHHHHHHHHhhCcccc
Confidence              45666666666666 2  333 34444433332332200 0000       1122567899999999988888653

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=95.02  E-value=0.35  Score=34.58  Aligned_cols=62  Identities=10%  Similarity=-0.014  Sum_probs=31.4

Q ss_pred             hhhHHHHHHHHHHcC--ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHh----hcc---chHHHHHHHHHHhh
Q 047113           16 VVIWSGMIASHAIHG--QEREALEAFYLVIHCSDGKPNNVTFLSILFAC----SYS---GLIEEGIKVFDIMV   79 (145)
Q Consensus        16 ~~~~~~li~a~~~~g--~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~----~~~---~~~~~a~~~~~~m~   79 (145)
                      ...||.--......|  ++++++++++.+.. ..-+ +...|+.--...    ...   ++++++..+++.+.
T Consensus        67 ~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~-~nPk-~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l  137 (306)
T 3dra_A           67 YTIWIYRFNILKNLPNRNLYDELDWCEEIAL-DNEK-NYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAML  137 (306)
T ss_dssp             HHHHHHHHHHHHTCTTSCHHHHHHHHHHHHH-HCTT-CCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccccHHHHHHHHHHHHH-HCcc-cHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHH
Confidence            345665555555555  66666666666554 2211 333444333333    222   45556666666555

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.82  E-value=0.22  Score=29.20  Aligned_cols=68  Identities=6%  Similarity=-0.063  Sum_probs=53.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhc-----CCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCS-----DGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN   87 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~-----~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~   87 (145)
                      ..+-.|-..+.+.|+++.|...|+...+..     .-.+....+..+-.++.+.|+++.|...+++.. +  +.|+
T Consensus         6 ~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al-~--l~P~   78 (104)
T 2v5f_A            6 EDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLL-E--LDPE   78 (104)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT
T ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHH-h--cCCC
Confidence            345578888999999999999999865412     123456788999999999999999999999988 3  4554

>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=94.59  E-value=0.14  Score=32.44  Aligned_cols=62  Identities=13%  Similarity=0.168  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           33 REALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        33 ~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      =+..+-++.+-. .++.|+.......+++|.+-+++..|.++|+-++.+.  .+...+|..+++-
T Consensus        70 wElrrglN~l~~-~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~--~~~~~iY~y~lqE  131 (152)
T 2y69_E           70 WELRKGMNTLVG-YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQE  131 (152)
T ss_dssp             HHHHHHHHHHTT-SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc--CCchhhHHHHHHH
Confidence            356666667667 8899999999999999999999999999999998443  4445667777653

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.25  E-value=0.51  Score=31.12  Aligned_cols=29  Identities=14%  Similarity=0.252  Sum_probs=21.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVI   43 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~   43 (145)
                      +...|..|-...-+.|+++-|.++|....
T Consensus        33 ~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~   61 (177)
T 3mkq_B           33 DSITWERLIQEALAQGNASLAEMIYQTQH   61 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHHhC
Confidence            45677777777777777777777777654

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=93.97  E-value=0.076  Score=39.75  Aligned_cols=34  Identities=3%  Similarity=-0.168  Sum_probs=23.4

Q ss_pred             hhhHHHHHHHHHhcc---ChhHHHHHHccCCCCCCCC
Q 047113          105 PYVWGALLGACRIHH---NVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus       105 ~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~  138 (145)
                      ...+..|-..|...|   +.++|...|++..+..+..
T Consensus       176 ~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~  212 (452)
T 3e4b_A          176 DICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVT  212 (452)
T ss_dssp             TTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHH
Confidence            336666777777777   7888888887766655544

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=93.93  E-value=0.35  Score=31.05  Aligned_cols=88  Identities=11%  Similarity=0.021  Sum_probs=45.0

Q ss_pred             HHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc---hHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHH
Q 047113           33 REALEAFYLVIHCSDGKPNNVTFLSILFACSYSG---LIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWG  109 (145)
Q Consensus        33 ~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~---~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~  109 (145)
                      ..+.+-|.+... .|- ++..+--..--+.++.+   ++++|..+++... +.. .|+ .              ....+=
T Consensus        15 ~~~~~~y~~e~~-~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll-~~~-~p~-~--------------~rd~lY   75 (152)
T 1pc2_A           15 LKFEKKFQSEKA-AGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELL-PKG-SKE-E--------------QRDYVF   75 (152)
T ss_dssp             HHHHHHHHHHHH-TTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHH-HHS-CHH-H--------------HHHHHH
T ss_pred             HHHHHHHHHHHc-cCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH-hcC-Ccc-c--------------hHHHHH
Confidence            344455554444 443 34333333333444444   6667777777776 322 121 0              011111


Q ss_pred             HHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113          110 ALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       110 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      .|--+|.+.|++++|++.++.+.+++|++.
T Consensus        76 ~LAv~~~kl~~Y~~A~~y~~~lL~ieP~n~  105 (152)
T 1pc2_A           76 YLAVGNYRLKEYEKALKYVRGLLQTEPQNN  105 (152)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHhcCCCCH
Confidence            123455777777777777777777777654

>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=93.85  E-value=0.34  Score=35.41  Aligned_cols=105  Identities=9%  Similarity=-0.004  Sum_probs=55.9

Q ss_pred             hhhHHHHHHHHHHcC-ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhcc-c-hHHHHHHHHHHhhhhcCcCccHHHHH
Q 047113           16 VVIWSGMIASHAIHG-QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYS-G-LIEEGIKVFDIMVHDFQLDLNLEHYG   92 (145)
Q Consensus        16 ~~~~~~li~a~~~~g-~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~-~-~~~~a~~~~~~m~~~~~~~~~~~~~~   92 (145)
                      -..||.--..+...| ++++++.+++.+.. .. +-+...|+.---...+. + +.+++..+++.+. .  ..       
T Consensus        88 ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~-~n-PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L-~--~d-------  155 (349)
T 3q7a_A           88 YTVWQYRFSLLTSLNKSLEDELRLMNEFAV-QN-LKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSL-L--PD-------  155 (349)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-TT-CCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHT-S--SC-------
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHH-hC-CCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHH-H--hC-------
Confidence            334554444444444 35555555555543 22 11334444443333333 3 4444444444444 1  11       


Q ss_pred             HHHHHHhcCCCchhhHHHHHHHHHhccChh--------HHHHHHccCCCCCCCCCCC
Q 047113           93 ITVDLLATGETEPYVWGALLGACRIHHNVK--------IGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        93 ~li~~~~~~~p~~~~~~~li~~~~~~g~~~--------~a~~~~~~~~~~~~~~~~~  141 (145)
                               +.+..+|+.-.-...+.|.++        ++++.++++.+.+|.+.+.
T Consensus       156 ---------pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~N~SA  203 (349)
T 3q7a_A          156 ---------PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGRNNSA  203 (349)
T ss_dssp             ---------TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTTCHHH
T ss_pred             ---------CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCCCHHH
Confidence                     336667776666666666666        8888888888877766544

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=93.74  E-value=0.54  Score=28.99  Aligned_cols=77  Identities=6%  Similarity=-0.108  Sum_probs=60.6

Q ss_pred             hHHHHhccCC-CCchhhHHHHHHHHHH----cCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc----cchHHHHHH
Q 047113            3 DAERIFGGII-DKNVVIWSGMIASHAI----HGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY----SGLIEEGIK   73 (145)
Q Consensus         3 ~A~~~f~~m~-~~~~~~~~~li~a~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~   73 (145)
                      +|.+.|+..- ..+...+..|-..|..    .+++++|.+.|+...+ .|   +...+..+-..+..    .+++++|..
T Consensus        43 ~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~-~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~  118 (138)
T 1klx_A           43 KLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACG-LN---DQDGCLILGYKQYAGKGVVKNEKQAVK  118 (138)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHc-CC---CHHHHHHHHHHHHCCCCCCcCHHHHHH
Confidence            4566666442 3577788888888888    8999999999999887 54   66777777777777    899999999


Q ss_pred             HHHHhhhhcCc
Q 047113           74 VFDIMVHDFQL   84 (145)
Q Consensus        74 ~~~~m~~~~~~   84 (145)
                      .|++.. +.|.
T Consensus       119 ~~~~Aa-~~g~  128 (138)
T 1klx_A          119 TFEKAC-RLGS  128 (138)
T ss_dssp             HHHHHH-HTTC
T ss_pred             HHHHHH-HCCC
Confidence            999998 6563

>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=93.29  E-value=0.73  Score=33.94  Aligned_cols=81  Identities=7%  Similarity=0.109  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhh----hcCcCccHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVH----DFQLDLNLEHYGIT   94 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~~~~~~l   94 (145)
                      ...++.++.+.|++++|...+..... .. +.+...|-.+|.++.+.|+..+|.+.|+.+..    +.|++|+..+-...
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~-~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~  251 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTF-EH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALN  251 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            34566778889999999999888755 22 34888999999999999999999999998763    45999988776655


Q ss_pred             HHHHhcC
Q 047113           95 VDLLATG  101 (145)
Q Consensus        95 i~~~~~~  101 (145)
                      -..+...
T Consensus       252 ~~il~~~  258 (388)
T 2ff4_A          252 ERILRQQ  258 (388)
T ss_dssp             HHHHTTC
T ss_pred             HHHHcCC
Confidence            5544443

>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=93.21  E-value=0.41  Score=34.22  Aligned_cols=88  Identities=13%  Similarity=0.020  Sum_probs=64.7

Q ss_pred             hHHHHhccCCC--C---chhhHHHHHHHHHHc-----CChHHHHHHHHHhHhhcCCCC--cHHHHHHHHHHhhcc-chHH
Q 047113            3 DAERIFGGIID--K---NVVIWSGMIASHAIH-----GQEREALEAFYLVIHCSDGKP--NNVTFLSILFACSYS-GLIE   69 (145)
Q Consensus         3 ~A~~~f~~m~~--~---~~~~~~~li~a~~~~-----g~~~~A~~~~~~m~~~~~~~p--~~~~~~~ll~~~~~~-~~~~   69 (145)
                      +|+..+++.-+  |   +-..|..|...|.+.     |+.++|.++|++-.+   +.|  +..++...-+.++.. |+.+
T Consensus       181 ~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~---LnP~~~id~~v~YA~~l~~~~gd~~  257 (301)
T 3u64_A          181 AAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTR---YCSAHDPDHHITYADALCIPLNNRA  257 (301)
T ss_dssp             HHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHH---HCCTTCSHHHHHHHHHTTTTTTCHH
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHH---hCCCCCchHHHHHHHHHHHhcCCHH
Confidence            34555554322  3   345899999999995     999999999999876   456  367777778888884 9999


Q ss_pred             HHHHHHHHhhhhcCcC--ccHHHHHHH
Q 047113           70 EGIKVFDIMVHDFQLD--LNLEHYGIT   94 (145)
Q Consensus        70 ~a~~~~~~m~~~~~~~--~~~~~~~~l   94 (145)
                      .+.+.+++.. .....  |+....+.+
T Consensus       258 ~a~~~L~kAL-~a~p~~~P~~~lan~~  283 (301)
T 3u64_A          258 GFDEALDRAL-AIDPESVPHNKLLVIL  283 (301)
T ss_dssp             HHHHHHHHHH-HCCGGGCSSCHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCCCCChhHHHHH
Confidence            9999999998 55544  655544443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=93.08  E-value=0.3  Score=28.62  Aligned_cols=78  Identities=10%  Similarity=-0.006  Sum_probs=56.5

Q ss_pred             cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHcc
Q 047113           51 NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKD  130 (145)
Q Consensus        51 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  130 (145)
                      +..-+-.+-..+-+.++++.|..-++.......-.++            ...+....+..|..+|.+.|++++|...+++
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~------------~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~   71 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEI------------STIDKVSVLDYLSYAVYQQGDLDKALLLTKK   71 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCC------------CSSCHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCC------------CcccHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            4445566777788899999999999887733211110            0123445678888999999999999999999


Q ss_pred             CCCCCCCCCC
Q 047113          131 PFHLDPKNDA  140 (145)
Q Consensus       131 ~~~~~~~~~~  140 (145)
                      ..+..|+++.
T Consensus        72 al~l~P~~~~   81 (104)
T 2v5f_A           72 LLELDPEHQR   81 (104)
T ss_dssp             HHHHCTTCHH
T ss_pred             HHhcCCCCHH
Confidence            9988887654

>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=92.48  E-value=0.73  Score=34.00  Aligned_cols=124  Identities=13%  Similarity=0.045  Sum_probs=75.3

Q ss_pred             CchhhHHHHHHHHHHc--C---ChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhcc--------chHHHHHHHHHHhh
Q 047113           14 KNVVIWSGMIASHAIH--G---QEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYS--------GLIEEGIKVFDIMV   79 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~--g---~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~--------~~~~~a~~~~~~m~   79 (145)
                      .+...|...+.+....  +   ...+|..+|++..+   +.|+ ...|..+.-++...        .......+.++...
T Consensus       192 ~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~---lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~  268 (372)
T 3ly7_A          192 HRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQ---SSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIV  268 (372)
T ss_dssp             SSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHH
Confidence            4677888888776542  2   35789999999866   4565 44555433333211        11112222222221


Q ss_pred             hhcCcCccHHHHHHHHHHHh-cC---------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           80 HDFQLDLNLEHYGITVDLLA-TG---------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        80 ~~~~~~~~~~~~~~li~~~~-~~---------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ....-..+..+|.++...+. +.               .|+...|..+-..+.-.|++++|.+.+++...++|..++
T Consensus       269 a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~t  345 (372)
T 3ly7_A          269 TLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGANT  345 (372)
T ss_dssp             TCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHHH
T ss_pred             hcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcCh
Confidence            11222445666666543332 12               777777777778888999999999999999999886553

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=92.45  E-value=0.89  Score=26.23  Aligned_cols=43  Identities=19%  Similarity=0.257  Sum_probs=35.4

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIH   44 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~   44 (145)
                      ++|.++|++..   +.++..+..+-..+.+.|++++|...|..+.+
T Consensus        26 ~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A           26 DEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            46777777553   34778888999999999999999999999976

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=87.34  E-value=4.1  Score=26.02  Aligned_cols=80  Identities=9%  Similarity=-0.020  Sum_probs=56.1

Q ss_pred             hHHHHhccC-C--CCchhhHHHHHHHHHHcC---ChHHHHHHHHHhHhhcCCCC---cHHHHHHHHHHhhccchHHHHHH
Q 047113            3 DAERIFGGI-I--DKNVVIWSGMIASHAIHG---QEREALEAFYLVIHCSDGKP---NNVTFLSILFACSYSGLIEEGIK   73 (145)
Q Consensus         3 ~A~~~f~~m-~--~~~~~~~~~li~a~~~~g---~~~~A~~~~~~m~~~~~~~p---~~~~~~~ll~~~~~~~~~~~a~~   73 (145)
                      ++++-|.+. .  .++..+.-.+-.++++.+   +.+++..+|++..+ .+ .|   ....|+.-+ ++.+.|+++.|.+
T Consensus        16 ~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~-~~-~p~~~rd~lY~LAv-~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           16 KFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLP-KG-SKEEQRDYVFYLAV-GNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHH-HS-CHHHHHHHHHHHHH-HHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHh-cC-CccchHHHHHHHHH-HHHHccCHHHHHH
Confidence            344445433 1  346667677777888888   67799999999877 44 34   223455544 5699999999999


Q ss_pred             HHHHhhhhcCcCccH
Q 047113           74 VFDIMVHDFQLDLNL   88 (145)
Q Consensus        74 ~~~~m~~~~~~~~~~   88 (145)
                      .++.+.   .++|+-
T Consensus        93 y~~~lL---~ieP~n  104 (152)
T 1pc2_A           93 YVRGLL---QTEPQN  104 (152)
T ss_dssp             HHHHHH---HHCTTC
T ss_pred             HHHHHH---hcCCCC
Confidence            999999   467753

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=87.17  E-value=8.1  Score=29.24  Aligned_cols=30  Identities=13%  Similarity=-0.088  Sum_probs=20.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIH   44 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~   44 (145)
                      +...|-..+.-+.+.|++++|..+|.+...
T Consensus       212 ~~~lW~~ya~~~~~~~~~~~ar~i~erAi~  241 (493)
T 2uy1_A          212 AEEVYFFYSEYLIGIGQKEKAKKVVERGIE  241 (493)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            445566666666677777777777776655

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=86.01  E-value=9.2  Score=30.07  Aligned_cols=55  Identities=15%  Similarity=0.033  Sum_probs=37.0

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +...|..|-..+.+.|+++.|.++|..+..          |..+...+...|+.+....+-+...
T Consensus       680 ~~~~W~~la~~al~~~~~~~A~~~y~~~~d----------~~~l~~l~~~~~~~~~~~~~~~~a~  734 (814)
T 3mkq_A          680 AEMKWRALGDASLQRFNFKLAIEAFTNAHD----------LESLFLLHSSFNNKEGLVTLAKDAE  734 (814)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC----------HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHhHHHHHHHHHHHcCCHHHHHHHHHHccC----------hhhhHHHHHHcCCHHHHHHHHHHHH
Confidence            456888888888888888888888887754          2334444445666665555544444

>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=84.75  E-value=4  Score=24.43  Aligned_cols=44  Identities=7%  Similarity=0.021  Sum_probs=35.9

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSIL   59 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll   59 (145)
                      |++.+..+.+.||.|.+++.-|.++|+..+.+.|-+  ..+|..++
T Consensus        43 P~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~--~~iY~~~l   86 (109)
T 1v54_E           43 PEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPH--KEIYPYVI   86 (109)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTC--TTHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCc--hhhHHHHH
Confidence            788899999999999999999999999987634433  44677666

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=83.86  E-value=5.7  Score=24.52  Aligned_cols=91  Identities=10%  Similarity=0.023  Sum_probs=53.8

Q ss_pred             ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc---cchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhh
Q 047113           31 QEREALEAFYLVIHCSDGKPNNVTFLSILFACSY---SGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYV  107 (145)
Q Consensus        31 ~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~---~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~  107 (145)
                      ....+.+-|..... .|-......|+-.. +..+   ..+..++..+++.+. +.+ .|.                ...-
T Consensus        16 ~l~~~~~~y~~e~~-~~~~s~~~~F~yAw-~Lv~S~~~~d~~~GI~lLe~l~-~~~-~p~----------------~~Rd   75 (126)
T 1nzn_A           16 DLLKFEKKFQSEKA-AGSVSKSTQFEYAW-CLVRTRYNDDIRKGIVLLEELL-PKG-SKE----------------EQRD   75 (126)
T ss_dssp             HHHHHHHHHHHHHH-HSCCCHHHHHHHHH-HHTTSSSHHHHHHHHHHHHHHT-TTS-CHH----------------HHHH
T ss_pred             HHHHHHHHHHHHhc-cCCCcHHHHHHHHH-HHHcCCCHHHHHHHHHHHHHHH-hcC-Ccc----------------hHHH
Confidence            34455555655544 44432333444332 3333   335566889998888 433 121                1111


Q ss_pred             HH-HHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          108 WG-ALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       108 ~~-~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +. .|--|+.+.|++++|++.++.+.+.+|++...
T Consensus        76 ~lY~LAvg~yklg~Y~~A~~~~~~lL~~eP~n~QA  110 (126)
T 1nzn_A           76 YVFYLAVGNYRLKEYEKALKYVRGLLQTEPQNNQA  110 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHH
Confidence            11 23467899999999999999999999977543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=82.87  E-value=13  Score=28.04  Aligned_cols=111  Identities=6%  Similarity=-0.009  Sum_probs=67.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHH--HHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFL--SILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~--~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ..|-..+...-+.+..+.|..+|..... .+  ++...|.  +.+.... .++.+.|..+|+...+..+-.  ...|...
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A~~-~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~~~~--~~~~~~y  360 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIELGN-EG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKHPDS--TLLKEEF  360 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHTT-SC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHCTTC--HHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhhC-CC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHCCCC--HHHHHHH
Confidence            4577777777778889999999988722 22  2333332  3333322 236889999999888443222  3334444


Q ss_pred             HHHHhcC-------------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           95 VDLLATG-------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        95 i~~~~~~-------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ++...+.             ......|...+.-=...|+.+.+..++++...
T Consensus       361 id~e~~~~~~~~aR~l~er~~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          361 FLFLLRIGDEENARALFKRLEKTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHHHTCHHHHHHHHHHSCCBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4432222             22345677777655677888888887776553

>3ygs_P Procaspase 9; apoptosis, caspase activation, caspase recruitment, recognition complex; 2.50A {Homo sapiens} SCOP: a.77.1.3

Probab=82.11  E-value=1.7  Score=25.40  Aligned_cols=40  Identities=5%  Similarity=-0.085  Sum_probs=25.6

Q ss_pred             CChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHH
Q 047113           30 GQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKV   74 (145)
Q Consensus        30 g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~   74 (145)
                      .+.++|.++++.+.. .|    ...|...+++..+.|+...|..+
T Consensus        51 t~~~~ar~Lld~L~~-rG----~~Af~~F~~aL~et~~~~La~lL   90 (97)
T 3ygs_P           51 SRRDQARQLIIDLET-RG----SQALPLFISCLEDTGQDMLASFL   90 (97)
T ss_dssp             CHHHHHHHHHHHHTT-SC----TTHHHHHHHHHHTTTCHHHHHHH
T ss_pred             ChHHHHHHHHHHHHH-cC----hHHHHHHHHHHHHcCcHHHHHHH
Confidence            467777788877765 33    35667777777666665555433

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=82.04  E-value=3.7  Score=26.02  Aligned_cols=58  Identities=10%  Similarity=0.005  Sum_probs=39.1

Q ss_pred             ccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhH-HHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           64 YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVW-GALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~-~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ...+..++..+++.+. +.+  |.                +..-+ =.|--|+.+.|++++|++..+.+.+.+|++..
T Consensus        54 ~~~di~~GI~LLe~l~-~~~--~~----------------~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~eP~n~Q  112 (144)
T 1y8m_A           54 DVNDERLGVKILTDIY-KEA--ES----------------RRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQ  112 (144)
T ss_dssp             SHHHHHHHHHHHHHHH-HHC--CS----------------THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTCCCCHH
T ss_pred             CHHHHHHHHHHHHHHH-hcC--cc----------------chhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHH
Confidence            3456678888888887 422  21                11111 12345788999999999999999999887643

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=81.45  E-value=12  Score=26.40  Aligned_cols=111  Identities=13%  Similarity=0.004  Sum_probs=76.1

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhh-hcCcCccHHHHHHHHHHHhcC
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVH-DFQLDLNLEHYGITVDLLATG  101 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-~~~~~~~~~~~~~li~~~~~~  101 (145)
                      ....+.|..++|++....-.+ .  .| |...=..++..+|-.|+|++|..=++.... +-...|...+|..+|.+=...
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR-~--~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~aE~~R   81 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIK-A--SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQAR   81 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHH-T--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHH-h--CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHHHHHH
Confidence            345678999999998887654 2  45 777888999999999999999988887772 223455566777777543322


Q ss_pred             --------CC-----chhhHHHHHHHHHh--ccChhHHHHHHccCCCCCCC
Q 047113          102 --------ET-----EPYVWGALLGACRI--HHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus       102 --------~p-----~~~~~~~li~~~~~--~g~~~~a~~~~~~~~~~~~~  137 (145)
                              .|     ...-...++.+...  .|+.++|.++-..+.+.-|.
T Consensus        82 ~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~ap~  132 (273)
T 1zbp_A           82 KDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQE  132 (273)
T ss_dssp             HHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhcCcc
Confidence                    11     11233455566644  59999999988887665443

>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=81.13  E-value=2.6  Score=31.00  Aligned_cols=41  Identities=17%  Similarity=0.246  Sum_probs=35.4

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHh----hcCCCCcHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIH----CSDGKPNNVTF   55 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~----~~~~~p~~~~~   55 (145)
                      +...|..+|.++.+.|+..+|++.|+.+..    +.|+.|...+-
T Consensus       204 ~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          204 REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            667899999999999999999999998643    47999987763

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=80.15  E-value=4.8  Score=25.16  Aligned_cols=59  Identities=10%  Similarity=0.012  Sum_probs=40.7

Q ss_pred             ccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           64 YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      ...+...|..+++.+. +.+  |.               .....+=.|--|+.+.|++++|++..+.+.+.+|++..
T Consensus        55 ~~~d~~~GI~LLe~l~-~~~--~~---------------~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~N~Q  113 (134)
T 3o48_A           55 DVNDERLGVKILTDIY-KEA--ES---------------RRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQ  113 (134)
T ss_dssp             CHHHHHHHHHHHHHHH-HHC--GG---------------GHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTTCHH
T ss_pred             CHHHHHHHHHHHHHHH-hcC--cc---------------hhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCCHH
Confidence            3446778888888887 433  21               01122223456888999999999999999999997653

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A

Probab=80.13  E-value=8.1  Score=23.74  Aligned_cols=101  Identities=7%  Similarity=-0.007  Sum_probs=61.7

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccc--hHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSG--LIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .-+.+|.-|...|+.++|.++++++.. -.+. .......+..+.-+.+  ..+....++..+. ..|+-+.......+-
T Consensus         9 ki~~ll~EY~~~~D~~Ea~~cl~eL~~-p~f~-~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~-~~~~is~~q~~~Gf~   85 (129)
T 2nsz_A            9 EIDMLLKEYLLSGDISEAEHCLKELEV-PHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLW-KSSTITIDQMKRGYE   85 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTC-GGGH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHH-HTTCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhCC-CccH-HHHHHHHHHHHHcCCChHHHHHHHHHHHHHH-HCCCcCHHHHHHHHH
Confidence            356789999999999999999999864 2222 2334455555665543  3567888888887 677665544433333


Q ss_pred             HHHhcC------CCchhhH-HHHHHHHHhccCh
Q 047113           96 DLLATG------ETEPYVW-GALLGACRIHHNV  121 (145)
Q Consensus        96 ~~~~~~------~p~~~~~-~~li~~~~~~g~~  121 (145)
                      ..+...      .|....+ ..++.-+...|-+
T Consensus        86 ~v~~~l~Dl~lDiP~a~~~l~~~v~~ai~~g~l  118 (129)
T 2nsz_A           86 RIYNEIPDINLDVPHSYSVLERFVEECFQAGII  118 (129)
T ss_dssp             HHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTCS
T ss_pred             HHHhhChHhhcCccchHHHHHHHHHHHHHCCCC
Confidence            333332      6666543 3334444444443

---

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	145
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.94
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.77
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.67
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.63
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.58
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.57
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.56
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.44
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.41
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.4
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.3
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.23
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.21
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.2
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.17
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.12
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.08
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.05
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	97.89
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.85
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.84
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.84
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.79
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.77
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.76
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.72
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.7
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.64
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.61
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.49
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.27
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.2
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.18
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.05
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.03
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.02
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.79
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.79
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.78
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.51
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	96.42
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.41
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.31
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.13
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.05
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.0
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	95.58
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	95.42
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.4
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.37
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	92.96
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	92.35
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	89.48
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	87.8
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	85.28
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	85.23
d1ug3a1	193	Eukaryotic initiation factor eIF4G {Human (Homo sa	85.06

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=5.4e-09  Score=73.38  Aligned_cols=136  Identities=10%  Similarity=0.108  Sum_probs=92.0

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+...   ..+...|..+...+.+.|++++|...|++..+   +.| +...+..+...+...|++++|...++.
T Consensus       220 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~  296 (388)
T d1w3ba_         220 DRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIE---LQPHFPDAYCNLANALKEKGSVAEAEDCYNT  296 (388)
T ss_dssp             THHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             HHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence            45555555442   23455677777777777777777777777654   234 456777777777777777777777777


Q ss_pred             hhhhcCcCccHHHHHHHHHHHhcC----------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGITVDLLATG----------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~li~~~~~~----------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      .. . ..+.+...+..+...|.+.                .| +..+|..+-..|...|++++|...+++..+++|+++.
T Consensus       297 ~~-~-~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~~  374 (388)
T d1w3ba_         297 AL-R-LCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFAD  374 (388)
T ss_dssp             HH-H-HCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHH
T ss_pred             hh-c-cCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHH
Confidence            66 2 2234556666666666655                33 4567777888888888888888888888888887665


Q ss_pred             Cc
Q 047113          141 YY  142 (145)
Q Consensus       141 ~~  142 (145)
                      .|
T Consensus       375 a~  376 (388)
T d1w3ba_         375 AY  376 (388)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=4.3e-08  Score=68.63  Aligned_cols=136  Identities=13%  Similarity=0.043  Sum_probs=109.3

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...++..   .+.+...|..+...+...|++++|...|..... .+ ..+...+..+-..+.+.|+++.|...|++.
T Consensus       186 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  263 (388)
T d1w3ba_         186 WLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALS-LS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRA  263 (388)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHH-Hh-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3455556533   234667899999999999999999999999876 43 336677888888999999999999999998


Q ss_pred             hhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           79 VHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        79 ~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                      . .  +.| +...|..+..+|.+.                 +.+...+..+...+...|++++|...+++..+..|+++.
T Consensus       264 l-~--~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~  340 (388)
T d1w3ba_         264 I-E--LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAA  340 (388)
T ss_dssp             H-H--TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHH
T ss_pred             H-H--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH
Confidence            7 3  344 467788887777755                 556788999999999999999999999999999998765


Q ss_pred             Cc
Q 047113          141 YY  142 (145)
Q Consensus       141 ~~  142 (145)
                      .+
T Consensus       341 ~~  342 (388)
T d1w3ba_         341 AH  342 (388)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=98.67  E-value=6.6e-08  Score=62.88  Aligned_cols=106  Identities=8%  Similarity=-0.089  Sum_probs=85.9

Q ss_pred             CchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           14 KNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        14 ~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      |+...+...-..+.+.|++++|+..|..... .. +-+...|+.+-.++.+.|+++.|...|+...   .+.|+      
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~-~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al---~l~p~------   70 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAIT-RN-PLVAVYYTNRALCYLKMQQPEQALADCRRAL---ELDGQ------   70 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHT---TSCTT------
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHH---HhCCC------
Confidence            5556677778899999999999999998765 32 2367889999999999999999999999998   34554      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                                +..+|..+-.+|.+.|++++|+..|++..++.|+...
T Consensus        71 ----------~~~a~~~lg~~~~~l~~~~~A~~~~~~al~l~p~~~~  107 (201)
T d2c2la1          71 ----------SVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRL  107 (201)
T ss_dssp             ----------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             ----------cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHH
Confidence                      5567777888999999999999999987776664443

>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=98.63  E-value=2.7e-07  Score=62.05  Aligned_cols=132  Identities=14%  Similarity=-0.104  Sum_probs=96.2

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..   .+.+..+|+.+-.++.+.|++++|+..|++..+   +.| +..++..+-.++...|+++.|...|+.
T Consensus        54 ~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~  130 (259)
T d1xnfa_          54 ALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLE---LDPTYNYAHLNRGIALYYGGRDKLAQDDLLA  130 (259)
T ss_dssp             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHH---HHhhhhhhHHHHHHHHHHHhhHHHHHHHHHH
Confidence            5677777744   345788999999999999999999999999876   345 466788888889999999999999998


Q ss_pred             hhhhcCcCc-cHHHHHHHHHHHhcC----------------------------------------------------CCc
Q 047113           78 MVHDFQLDL-NLEHYGITVDLLATG----------------------------------------------------ETE  104 (145)
Q Consensus        78 m~~~~~~~~-~~~~~~~li~~~~~~----------------------------------------------------~p~  104 (145)
                      .. +.  .| +......+...+.+.                                                    .|+
T Consensus       131 al-~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  207 (259)
T d1xnfa_         131 FY-QD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEH  207 (259)
T ss_dssp             HH-HH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHH
T ss_pred             HH-hh--ccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcc
Confidence            87 32  22 222211111111111                                                    222


Q ss_pred             -hhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113          105 -PYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus       105 -~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                       ..+|..+-..|...|++++|...|++.....|++-
T Consensus       208 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~  243 (259)
T d1xnfa_         208 LSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNF  243 (259)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTC
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCH
Confidence             34677788899999999999999999988888653

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=2.9e-07  Score=63.80  Aligned_cols=75  Identities=17%  Similarity=0.283  Sum_probs=61.9

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..-   +.+..+|..+..++.+.|++++|...|.+..+   +.| +...|..+...+...|+++.|...++.
T Consensus        36 ~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~  112 (323)
T d1fcha_          36 PNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLE---LKPDNQTALMALAVSFTNESLQRQACEILRD  112 (323)
T ss_dssp             HHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhc---cccccccccccccccccccccccccccchhh
Confidence            57888888653   23677899999999999999999999999765   345 577888888899999999999988887


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus       113 ~~  114 (323)
T d1fcha_         113 WL  114 (323)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>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=98.57  E-value=1.7e-07  Score=56.62  Aligned_cols=100  Identities=14%  Similarity=0.047  Sum_probs=84.8

Q ss_pred             HHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhc
Q 047113           21 GMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLAT  100 (145)
Q Consensus        21 ~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  100 (145)
                      .--..+.+.|++++|+.+|++..+ .. +-+...|..+-.++...|+++.|...+.... .  +.|              
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~-~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al-~--~~p--------------   68 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIK-LD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTV-D--LKP--------------   68 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-H--HCT--------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh-cC-CcchhhhhcccccccccccccccchhhhhHH-H--hcc--------------
Confidence            345678899999999999999876 33 3367889999999999999999999999998 3  333              


Q ss_pred             CCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          101 GETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       101 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                        .+...|..+..++...|++++|...+++..+..|+++..
T Consensus        69 --~~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~p~~~~~  107 (117)
T d1elwa_          69 --DWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQL  107 (117)
T ss_dssp             --TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHH
T ss_pred             --chhhHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHH
Confidence              367788889999999999999999999999999987654

>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=98.56  E-value=1.4e-06  Score=60.63  Aligned_cols=133  Identities=8%  Similarity=0.080  Sum_probs=97.1

Q ss_pred             chHHHHhccC----CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI----IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m----~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.++|+..    .+.+...|.......-+.|++++|..+|+.+.. ..-......|...+..+.+.|+++.|..+|+.
T Consensus        81 ~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~-~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~  159 (308)
T d2onda1          81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA-IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  159 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH-HhcCChHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            4567777753    234666889899999999999999999999865 33222345789999999999999999999999


Q ss_pred             hhhhcCcCccHHHHHH--HHHHHhc-C---------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           78 MVHDFQLDLNLEHYGI--TVDLLAT-G---------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        78 m~~~~~~~~~~~~~~~--li~~~~~-~---------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                      .. +.+ +.+...|..  .+.-+.. .               +.+...|...++-..+.|+++.|+.+|++..+..|.
T Consensus       160 al-~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~  235 (308)
T d2onda1         160 AR-EDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  235 (308)
T ss_dssp             HH-TST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSS
T ss_pred             HH-HhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC
Confidence            88 322 223333333  3322221 1               556778999999999999999999999997665443

>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=98.44  E-value=8.5e-07  Score=55.97  Aligned_cols=101  Identities=6%  Similarity=-0.046  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLL   98 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~   98 (145)
                      +...-..|.+.|++++|...|....+ .. +-+...|..+-.++...|+++.|...|+... +.  .|+           
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~-~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal-~~--~p~-----------   76 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIE-LN-PSNAIYYGNRSLAYLRTECYGYALGDATRAI-EL--DKK-----------   76 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--CTT-----------
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccc-cc-hhhhhhhhhhHHHHHhccccchHHHHHHHHH-HH--ccc-----------
Confidence            44556678899999999999998876 43 2267788888889999999999999999888 32  332           


Q ss_pred             hcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCC
Q 047113           99 ATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDA  140 (145)
Q Consensus        99 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  140 (145)
                           +..+|..+..+|...|++++|...+++..++.|+++.
T Consensus        77 -----~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~~p~~~~  113 (159)
T d1a17a_          77 -----YIKGYYRRAASNMALGKFRAALRDYETVVKVKPHDKD  113 (159)
T ss_dssp             -----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHH
T ss_pred             -----chHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHH
Confidence                 5567777788888888888888888888777776654

>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=98.41  E-value=2.9e-06  Score=55.35  Aligned_cols=125  Identities=15%  Similarity=-0.026  Sum_probs=90.0

Q ss_pred             chHHHHhccCCCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhh
Q 047113            2 DDAERIFGGIIDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus         2 ~~A~~~f~~m~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      ++|.+.|+.+.+++..+|..+-..|...|++++|.+.|++..+ .+ +-+...|..+-.++.+.|+++.|...|++.. .
T Consensus        22 ~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~-ld-p~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl-~   98 (192)
T d1hh8a_          22 KGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSIN-RD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEAL-I   98 (192)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHH-Hh-hhhhhhHHHHHHHHHhhccHHHHHHHHHHHH-H
Confidence            5789999999889999999999999999999999999999876 33 2267799999999999999999999999876 2


Q ss_pred             cCcCccHHHHHHHHHHHhcC----CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           82 FQLDLNLEHYGITVDLLATG----ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        82 ~~~~~~~~~~~~li~~~~~~----~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                      .. ..+..     + .|...    .. ...++..+-.++...|++++|.+.+++..+..|
T Consensus        99 ~~-~~n~~-----~-~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~  151 (192)
T d1hh8a_          99 QL-RGNQL-----I-DYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKS  151 (192)
T ss_dssp             TT-TTCSE-----E-ECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             hC-ccCch-----H-HHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            11 11100     0 00000    11 123445556667777777777777776665544

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.40  E-value=4.2e-07  Score=62.96  Aligned_cols=105  Identities=10%  Similarity=0.096  Sum_probs=84.5

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      +...|..+...+.+.|++++|...|+.... .  .| +...|..+-..+.+.|+++.|...|++.. +  +.|+      
T Consensus       171 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~--~~p~------  238 (323)
T d1fcha_         171 DPDVQCGLGVLFNLSGEYDKAVDCFTAALS-V--RPNDYLLWNKLGATLANGNQSEEAVAAYRRAL-E--LQPG------  238 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT------
T ss_pred             ccccchhhHHHHHHHHHHhhhhcccccccc-c--ccccccchhhhhhcccccccchhHHHHHHHHH-H--Hhhc------
Confidence            556788888999999999999999998765 3  34 57788888899999999999999999887 3  2343      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                                +..+|..+..+|.+.|++++|...|++..++.|++...
T Consensus       239 ----------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~  276 (323)
T d1fcha_         239 ----------YIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGP  276 (323)
T ss_dssp             ----------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC---
T ss_pred             ----------cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhh
Confidence                      55678888899999999999999999988877765543

>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=98.30  E-value=2e-06  Score=57.58  Aligned_cols=101  Identities=15%  Similarity=0.052  Sum_probs=78.6

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGIT   94 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l   94 (145)
                      ..+|..+-..|.+.|++++|...|+...+   +.| +..+|+.+-.++.+.|+++.|...|++.. +  +.|+       
T Consensus        37 a~~~~~~G~~y~~~g~~~~A~~~~~~al~---l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al-~--~~p~-------  103 (259)
T d1xnfa_          37 AQLLYERGVLYDSLGLRALARNDFSQALA---IRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVL-E--LDPT-------  103 (259)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT-------
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHhhc---cCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHH-H--HHhh-------
Confidence            45788889999999999999999999866   356 67899999999999999999999999998 3  3443       


Q ss_pred             HHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           95 VDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        95 i~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                               +..+|..+...|...|++++|...+++..+..|.+
T Consensus       104 ---------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~  138 (259)
T d1xnfa_         104 ---------YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPND  138 (259)
T ss_dssp             ---------CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             ---------hhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhcccc
Confidence                     33455556666666777777777777666655544

>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=98.23  E-value=3.2e-06  Score=59.16  Aligned_cols=132  Identities=11%  Similarity=0.095  Sum_probs=68.2

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcC-ChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHG-QEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g-~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      ++|.++++..-   +.+...|+....++...| ++++|+..++...+   +.| +..+|+.+-..+.+.|++++|...++
T Consensus        60 ~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~---~~p~~~~a~~~~~~~~~~l~~~~eAl~~~~  136 (315)
T d2h6fa1          60 ERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE---EQPKNYQVWHHRRVLVEWLRDPSQELEFIA  136 (315)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHTCCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHH---HHHhhhhHHHHHhHHHHhhccHHHHHHHHh
Confidence            34555555332   224556666666666554 35666666666544   223 45566666666666666666666666


Q ss_pred             HhhhhcCcCc-cHHHHHHHHHHHhcC-----------------CCchhhHHHHHHHHHhccC------hhHHHHHHccCC
Q 047113           77 IMVHDFQLDL-NLEHYGITVDLLATG-----------------ETEPYVWGALLGACRIHHN------VKIGELVAKDPF  132 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~------~~~a~~~~~~~~  132 (145)
                      .+. .  +.| +...|..+...|.+.                 +.+...|+.+-..+.+.|.      +++|...+.+..
T Consensus       137 kal-~--~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al  213 (315)
T d2h6fa1         137 DIL-N--QDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMI  213 (315)
T ss_dssp             HHH-H--HCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHH
T ss_pred             hhh-h--hhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHH
Confidence            665 2  333 355555555444433                 2234455544444443333      345555555555


Q ss_pred             CCCCCCC
Q 047113          133 HLDPKND  139 (145)
Q Consensus       133 ~~~~~~~  139 (145)
                      +..|+++
T Consensus       214 ~~~P~~~  220 (315)
T d2h6fa1         214 KLVPHNE  220 (315)
T ss_dssp             HHSTTCH
T ss_pred             HhCCCch
Confidence            5555443

>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=98.21  E-value=2.6e-06  Score=51.72  Aligned_cols=103  Identities=9%  Similarity=-0.009  Sum_probs=77.1

Q ss_pred             HHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhc---cchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           20 SGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSY---SGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        20 ~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~---~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      ..+++.+...+++++|.+.|+.... .+ +.+..++..+-.++.+   .+++++|..+++... ..  .|+..       
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~-~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l-~~--~~~~~-------   70 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKA-AG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELL-PK--GSKEE-------   70 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-HS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHT-TT--SCHHH-------
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHh-hC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHH-hc--cCCch-------
Confidence            4678888999999999999999866 33 2356677777766665   456778999999987 32  23211       


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                             ...+|..|-.+|.+.|++++|+..|+++.+++|+++..
T Consensus        71 -------~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~~~P~~~~A  108 (122)
T d1nzna_          71 -------QRDYVFYLAVGNYRLKEYEKALKYVRGLLQTEPQNNQA  108 (122)
T ss_dssp             -------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             -------HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhCcCCHHH
Confidence                   12355667788999999999999999999999987543

>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=98.20  E-value=7.6e-06  Score=52.20  Aligned_cols=106  Identities=13%  Similarity=0.079  Sum_probs=81.7

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-------------cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcC
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-------------NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ   83 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-------------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~   83 (145)
                      ..+...-..+.+.|++++|+..|..........+             -..+|+.+-.+|.+.|+++.|...++... .  
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al-~--   90 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKAL-E--   90 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhh-h--
Confidence            4566677889999999999999988654112111             13466777888899999999999999888 3  


Q ss_pred             cCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           84 LDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        84 ~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +.|+                +...|..+..+|...|++++|...|++..++.|+++..
T Consensus        91 ~~p~----------------~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~  132 (170)
T d1p5qa1          91 LDSN----------------NEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAA  132 (170)
T ss_dssp             HCTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHH
T ss_pred             cccc----------------chhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHH
Confidence            2443                66677788889999999999999999998888877543

>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=98.17  E-value=3.3e-06  Score=59.11  Aligned_cols=121  Identities=8%  Similarity=-0.030  Sum_probs=99.8

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc-hHHHHHHHHHHhhhhcCcCc-cHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG-LIEEGIKVFDIMVHDFQLDL-NLEHYG   92 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~-~~~~a~~~~~~m~~~~~~~~-~~~~~~   92 (145)
                      ...|+.+-..+.+.+++++|+.+++...+   +.| +...|+..-.++...| ++++|...++... .  +.| +...|.
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~---lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al-~--~~p~~~~a~~  116 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIE---LNAANYTVWHFRRVLLKSLQKDLHEEMNYITAII-E--EQPKNYQVWH  116 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHH-H--HCTTCHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHH---HCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHH-H--HHHhhhhHHH
Confidence            34678888889999999999999999987   456 5668888888887766 5999999999987 2  345 577888


Q ss_pred             HHHHHHhcC-----------------CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           93 ITVDLLATG-----------------ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        93 ~li~~~~~~-----------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      .+...+.+.                 +.+...|..+...+...|++++|+..+++..+++|++...|
T Consensus       117 ~~~~~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~  183 (315)
T d2h6fa1         117 HRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVW  183 (315)
T ss_dssp             HHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHH
T ss_pred             HHhHHHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHH
Confidence            777777655                 55778999999999999999999999999999999876554

>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=98.12  E-value=1.2e-05  Score=47.73  Aligned_cols=91  Identities=18%  Similarity=-0.007  Sum_probs=76.4

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      +-.+-..+.+.|++++|...|+.... .  .| +...|..+-.++.+.|++++|...++... .  +.|+          
T Consensus        19 ~~~~g~~~~~~g~~~~A~~~~~~al~-~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al-~--~~p~----------   82 (112)
T d1hxia_          19 PMEEGLSMLKLANLAEAALAFEAVCQ-K--EPEREEAWRSLGLTQAENEKDGLAIIALNHAR-M--LDPK----------   82 (112)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH-H--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT----------
T ss_pred             HHHHHHHHHHHhhhHHHHHHHhhhcc-c--ccccchhhhhhhhhhhhhhhHHHhhccccccc-c--cccc----------
Confidence            33456778899999999999999876 3  45 68899999999999999999999999988 2  3443          


Q ss_pred             HhcCCCchhhHHHHHHHHHhccChhHHHHHHccC
Q 047113           98 LATGETEPYVWGALLGACRIHHNVKIGELVAKDP  131 (145)
Q Consensus        98 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  131 (145)
                            +..+|..+-..|...|++++|.+.+++.
T Consensus        83 ------~~~a~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          83 ------DIAVHAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ------cccchHHHHHHHHHCCCHHHHHHHHHHH
Confidence                  6678888899999999999999998763

>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=98.08  E-value=2.1e-05  Score=49.16  Aligned_cols=107  Identities=10%  Similarity=-0.069  Sum_probs=83.7

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCC---Cc-----------HHHHHHHHHHhhccchHHHHHHHHHHhhhh
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGK---PN-----------NVTFLSILFACSYSGLIEEGIKVFDIMVHD   81 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~---p~-----------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~   81 (145)
                      ..++......+.+.|++++|+..|.+........   ++           ..+|+.+-.++.+.|+++.|...+.... .
T Consensus        17 a~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al-~   95 (153)
T d2fbna1          17 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVL-K   95 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccc-c
Confidence            3467778889999999999999999864301111   11           2467778888899999999999999887 2


Q ss_pred             cCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           82 FQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        82 ~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                        +.|+                +..+|..+..++...|++++|...|++..+++|+++..
T Consensus        96 --~~p~----------------~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~  137 (153)
T d2fbna1          96 --IDKN----------------NVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDI  137 (153)
T ss_dssp             --HSTT----------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHH
T ss_pred             --ccch----------------hhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH
Confidence              3343                66788889999999999999999999999999977643

>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=98.05  E-value=1.6e-05  Score=51.65  Aligned_cols=94  Identities=15%  Similarity=0.060  Sum_probs=77.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDL   97 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~   97 (145)
                      -||- -..+...|++++|++.|.++.     .|+...|..+-.++...|+++.|...|++.. +  +.|+          
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~-----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl-~--ldp~----------   68 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSI-N--RDKH----------   68 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--HCTT----------
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcC-----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHH-H--Hhhh----------
Confidence            4654 556689999999999998753     4778888899999999999999999999998 3  3443          


Q ss_pred             HhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           98 LATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        98 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                            +...|..+-.+|.+.|++++|...|++.....+
T Consensus        69 ------~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~  101 (192)
T d1hh8a_          69 ------LAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLR  101 (192)
T ss_dssp             ------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTT
T ss_pred             ------hhhhHHHHHHHHHhhccHHHHHHHHHHHHHhCc
Confidence                  667888888999999999999999988665433

>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=97.89  E-value=0.00017  Score=49.69  Aligned_cols=133  Identities=11%  Similarity=0.081  Sum_probs=96.2

Q ss_pred             chHHHHhccCCC--C-c-hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHH-HHhhccchHHHHHHHHH
Q 047113            2 DDAERIFGGIID--K-N-VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSIL-FACSYSGLIEEGIKVFD   76 (145)
Q Consensus         2 ~~A~~~f~~m~~--~-~-~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll-~~~~~~~~~~~a~~~~~   76 (145)
                      ++|..+|+.+..  | + ...|...+....+.|..++|.++|....+ ..-. +...|.... --....|+.+.|..+|+
T Consensus       116 ~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~-~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e  193 (308)
T d2onda1         116 EKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE-DART-RHHVYVTAALMEYYCSKDKSVAFKIFE  193 (308)
T ss_dssp             HHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT-STTC-CTHHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHH-hCCC-cHHHHHHHHHHHHHhccCHHHHHHHHH
Confidence            567888886532  2 3 34799999999999999999999999876 3322 333333322 23445688999999999


Q ss_pred             HhhhhcCcCccHHHHHHHHHHHhcC-------------------CCc--hhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           77 IMVHDFQLDLNLEHYGITVDLLATG-------------------ETE--PYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        77 ~m~~~~~~~~~~~~~~~li~~~~~~-------------------~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      .+. .. ...+...|...++.+.+.                   .|+  ...|...+.--...|+.+.+..+.+++.+..
T Consensus       194 ~~l-~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~  271 (308)
T d2onda1         194 LGL-KK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF  271 (308)
T ss_dssp             HHH-HH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHT
T ss_pred             HHH-Hh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            998 32 344678888888877766                   222  2468888887788899999999999887755


Q ss_pred             CCC
Q 047113          136 PKN  138 (145)
Q Consensus       136 ~~~  138 (145)
                      |..
T Consensus       272 ~~~  274 (308)
T d2onda1         272 REE  274 (308)
T ss_dssp             TTT
T ss_pred             ccc
Confidence            544

>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=97.85  E-value=3.7e-05  Score=52.56  Aligned_cols=109  Identities=16%  Similarity=0.048  Sum_probs=76.3

Q ss_pred             HHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHHHHHhcC---
Q 047113           27 AIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITVDLLATG---  101 (145)
Q Consensus        27 ~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~---  101 (145)
                      .+.|++++|+..|++-.+   ..| |...+..+...++..|++++|...++... +  ..|+ ...+..+...+...   
T Consensus         7 L~~G~l~eAl~~l~~al~---~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~-~--l~P~~~~~~~~l~~ll~a~~~~   80 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIK---ASPKDASLRSSFIELLCIDGDFERADEQLMQSI-K--LFPEYLPGASQLRHLVKAAQAR   80 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHH---TCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-H--HCGGGHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H--hCCCcHHHHHHHHHHHHhcccc
Confidence            356888999999888765   345 67788888888999999999988888887 2  3443 33433333332211   


Q ss_pred             --------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113          102 --------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus       102 --------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                                    .| +...+......+.+.|+.++|.+.++.+.+..|..+..
T Consensus        81 ~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p~~~~~  135 (264)
T d1zbpa1          81 KDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKGFL  135 (264)
T ss_dssp             HHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCCEE
T ss_pred             HHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCcc
Confidence                          23 33444555667788999999999999988877766543

>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=97.84  E-value=1.7e-05  Score=50.21  Aligned_cols=105  Identities=9%  Similarity=-0.040  Sum_probs=81.2

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhh-------------cCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcC
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHC-------------SDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ   83 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~-------------~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~   83 (145)
                      .+......+.+.|++++|+..|.+....             ..+.| +...|+.+-.++.+.|+++.|...+....   .
T Consensus        29 ~~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al---~  105 (169)
T d1ihga1          29 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEAL---E  105 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH---T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhh---h
Confidence            3556677888999999999999876320             11233 44467777888899999999999999988   2


Q ss_pred             cCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           84 LDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        84 ~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +.|+                +...|..+-.++.+.|++++|...|++..++.|+++..
T Consensus       106 ~~p~----------------~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~  147 (169)
T d1ihga1         106 IDPS----------------NTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAI  147 (169)
T ss_dssp             TCTT----------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             hhhh----------------hhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHH
Confidence            4443                66678888899999999999999999999999877543

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=0.00023  Score=42.12  Aligned_cols=87  Identities=18%  Similarity=0.147  Sum_probs=70.7

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      ++|...|++.-   +.+...|+.+-.++.+.|++++|+..|....+ .+ +.+...|..+-.++...|+++.|...|+..
T Consensus        20 ~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~-~~-p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a   97 (117)
T d1elwa_          20 DDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVD-LK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEG   97 (117)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHH-hc-cchhhHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            57888888652   34778999999999999999999999999876 43 347889999999999999999999999999


Q ss_pred             hhhcCcCcc-HHHHHH
Q 047113           79 VHDFQLDLN-LEHYGI   93 (145)
Q Consensus        79 ~~~~~~~~~-~~~~~~   93 (145)
                      .   .+.|+ ...+..
T Consensus        98 ~---~~~p~~~~~~~~  110 (117)
T d1elwa_          98 L---KHEANNPQLKEG  110 (117)
T ss_dssp             H---TTCTTCHHHHHH
T ss_pred             H---HhCCCCHHHHHH
Confidence            8   34554 333333

>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=97.79  E-value=5e-05  Score=48.04  Aligned_cols=107  Identities=11%  Similarity=0.010  Sum_probs=81.2

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-------------cHHHHHHHHHHhhccchHHHHHHHHHHhhhhc
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-------------NNVTFLSILFACSYSGLIEEGIKVFDIMVHDF   82 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-------------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~   82 (145)
                      ...+.-....+.+.|++++|...|..........+             ....|+.+-.++.+.|+++.|...++... . 
T Consensus        15 a~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al-~-   92 (168)
T d1kt1a1          15 AAIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKAL-G-   92 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H-
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhh-h-
Confidence            45677788899999999999999987432011111             12345566677888999999999999888 2 


Q ss_pred             CcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           83 QLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        83 ~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                       +.|                .+..+|..+..++...|++++|...|.+..+++|+++..
T Consensus        93 -l~p----------------~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~  134 (168)
T d1kt1a1          93 -LDS----------------ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAA  134 (168)
T ss_dssp             -HCT----------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHH
T ss_pred             -ccc----------------chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH
Confidence             334                366777888899999999999999999999999987644

>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=97.77  E-value=6.6e-05  Score=45.38  Aligned_cols=104  Identities=8%  Similarity=-0.060  Sum_probs=78.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHHHHHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYGITVD   96 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~   96 (145)
                      .+..+-+.+.+.|++++|+..|.+..+ .+ +.+...+..+-.++.+.|+++.|.+.++....   +.|+ ...|..+. 
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~-~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~---l~~~~~~~~~~~a-   79 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKE-LD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIE---VGRENREDYRQIA-   79 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HHHHSTTCHHHHH-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH-hC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHH---hCcccHHHHHHHH-
Confidence            456778899999999999999999877 43 23688999999999999999999999999882   2221 12222222 


Q ss_pred             HHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           97 LLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        97 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                               .+|..+-..+...+++++|...|++.....+
T Consensus        80 ---------~~~~~lg~~~~~~~~~~~A~~~~~kal~~~~  110 (128)
T d1elra_          80 ---------KAYARIGNSYFKEEKYKDAIHFYNKSLAEHR  110 (128)
T ss_dssp             ---------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC
T ss_pred             ---------HHHHHHHHHHHHhCCHHHHHHHHHHHHhcCC
Confidence                     3556677888888999999999887554433

>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=97.76  E-value=6.1e-05  Score=44.46  Aligned_cols=75  Identities=9%  Similarity=0.116  Sum_probs=63.8

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|...|+...   +.+...|..+-.++.+.|++++|...|+...+   +.| +...|..+-..+...|++++|.+.+++
T Consensus        33 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~a~~~la~~y~~~g~~~~A~~~l~~  109 (112)
T d1hxia_          33 AEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARM---LDPKDIAVHAALAVSHTNEHNANAALASLRA  109 (112)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccc---cccccccchHHHHHHHHHCCCHHHHHHHHHH
Confidence            46777777653   34688999999999999999999999999866   345 578999999999999999999999987


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus       110 ~l  111 (112)
T d1hxia_         110 WL  111 (112)
T ss_dssp             HH
T ss_pred             Hh
Confidence            64

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.72  E-value=8.1e-05  Score=47.59  Aligned_cols=75  Identities=11%  Similarity=-0.027  Sum_probs=65.4

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|.+.|+..   .+.+...|+.+-.+|.+.|++++|+..|....+   +.| +..+|..+-.++.+.|+++.|...|+.
T Consensus        21 ~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~---l~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~   97 (201)
T d2c2la1          21 PEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE---LDGQSVKAHFFLGQCQLEMESYDEAIANLQR   97 (201)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT---SCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH---hCCCcHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            5788888754   345788999999999999999999999999855   567 577999999999999999999999998


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus        98 al   99 (201)
T d2c2la1          98 AY   99 (201)
T ss_dssp             HH
T ss_pred             HH
Confidence            76

>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=97.70  E-value=0.00024  Score=44.19  Aligned_cols=75  Identities=11%  Similarity=0.070  Sum_probs=65.0

Q ss_pred             chHHHHhccCC---CCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHH
Q 047113            2 DDAERIFGGII---DKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDI   77 (145)
Q Consensus         2 ~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~   77 (145)
                      ++|...|...-   +.+...|..+-..+.+.|++++|...|+...+ .  .| +...|..+..++...|++++|...+++
T Consensus        27 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~-~--~p~~~~a~~~~g~~~~~~g~~~eA~~~~~~  103 (159)
T d1a17a_          27 ENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIE-L--DKKYIKGYYRRAASNMALGKFRAALRDYET  103 (159)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHH-H--cccchHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            56777777553   45788999999999999999999999999876 3  45 568999999999999999999999999


Q ss_pred             hh
Q 047113           78 MV   79 (145)
Q Consensus        78 m~   79 (145)
                      ..
T Consensus       104 a~  105 (159)
T d1a17a_         104 VV  105 (159)
T ss_dssp             HH
T ss_pred             HH
Confidence            98

>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=97.64  E-value=0.00018  Score=46.15  Aligned_cols=74  Identities=8%  Similarity=0.155  Sum_probs=63.8

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhh----hcCcCccHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVH----DFQLDLNLEHY   91 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~~~~   91 (145)
                      ..+..+..++.+.|++++|+..++....   +.| +...|..++.++.+.|+..+|.+.|+++..    ..|++|+..+-
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~---~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTF---EHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHH---hCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            4688999999999999999999999876   345 788999999999999999999999998852    46999987764


Q ss_pred             HH
Q 047113           92 GI   93 (145)
Q Consensus        92 ~~   93 (145)
                      ..
T Consensus       145 ~l  146 (179)
T d2ff4a2         145 AL  146 (179)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=97.61  E-value=7.7e-05  Score=51.77  Aligned_cols=135  Identities=14%  Similarity=0.019  Sum_probs=86.0

Q ss_pred             hHHHHhccCC---CCchhhHHHHHHHHHHcCC--hHHHHHHHHHhHhhcCCCCcHHHHHH-HHHHhhccchHHHHHHHHH
Q 047113            3 DAERIFGGII---DKNVVIWSGMIASHAIHGQ--EREALEAFYLVIHCSDGKPNNVTFLS-ILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m~---~~~~~~~~~li~a~~~~g~--~~~A~~~~~~m~~~~~~~p~~~~~~~-ll~~~~~~~~~~~a~~~~~   76 (145)
                      +|...|+..-   +.+...|..+..++...++  +++|...+....+ .. +++...+.. .-..+...+.++.|...++
T Consensus        91 ~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~-~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~  168 (334)
T d1dcea1          91 AELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLE-AD-ERNFHCWDYRRFVAAQAAVAPAEELAFTD  168 (334)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHh-hC-chhhhhhhhHHHHHHHhccccHHHHHHHH
Confidence            4555555442   2355667777666666554  6777777777755 32 223444433 3345556777777777777


Q ss_pred             HhhhhcCcCc-cHHHHHHHHHHHhcC------------------------------------------------------
Q 047113           77 IMVHDFQLDL-NLEHYGITVDLLATG------------------------------------------------------  101 (145)
Q Consensus        77 ~m~~~~~~~~-~~~~~~~li~~~~~~------------------------------------------------------  101 (145)
                      ... .  ..| +...|+.+..+|.+.                                                      
T Consensus       169 ~~i-~--~~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~  245 (334)
T d1dcea1         169 SLI-T--RNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRC  245 (334)
T ss_dssp             TTT-T--TTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSC
T ss_pred             HHH-H--cCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHH
Confidence            766 2  233 455555555544432                                                      


Q ss_pred             --------------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113          102 --------------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus       102 --------------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                                                .| +..+|..+...+...|++++|...+++..+++|+.+.+|
T Consensus       246 ~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~  313 (334)
T d1dcea1         246 ELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYL  313 (334)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcccHHHH
Confidence                                      23 446788888899999999999999999999998765543

>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=97.49  E-value=0.00019  Score=43.18  Aligned_cols=84  Identities=7%  Similarity=-0.053  Sum_probs=63.7

Q ss_pred             CchHHHHhccCC---CCchhhHHHHHHHHHHcCCh---HHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHH
Q 047113            1 MDDAERIFGGII---DKNVVIWSGMIASHAIHGQE---REALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIK   73 (145)
Q Consensus         1 ~~~A~~~f~~m~---~~~~~~~~~li~a~~~~g~~---~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~   73 (145)
                      +++|++.|+...   +.+..++..+-.++.+.++.   ++|+.+|+.... .+-.|+ ..++..+-.+|.+.|+++.|..
T Consensus        15 l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~-~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~   93 (122)
T d1nzna_          15 LLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLP-KGSKEEQRDYVFYLAVGNYRLKEYEKALK   93 (122)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTT-TSCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHh-ccCCchHHHHHHHHHHHHHHHhhhHHHHH
Confidence            367888888653   45778888888888876654   569999998765 443333 2367778889999999999999


Q ss_pred             HHHHhhhhcCcCccH
Q 047113           74 VFDIMVHDFQLDLNL   88 (145)
Q Consensus        74 ~~~~m~~~~~~~~~~   88 (145)
                      .|++.. +  +.|+-
T Consensus        94 ~~~~aL-~--~~P~~  105 (122)
T d1nzna_          94 YVRGLL-Q--TEPQN  105 (122)
T ss_dssp             HHHHHH-H--HCTTC
T ss_pred             HHHHHH-H--hCcCC
Confidence            999999 3  56753

>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=97.27  E-value=0.0019  Score=41.16  Aligned_cols=95  Identities=9%  Similarity=-0.077  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhcC--CCCc------------------HHHHHHHHHHhhccchHHHHHHHHHHh
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCSD--GKPN------------------NVTFLSILFACSYSGLIEEGIKVFDIM   78 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~~--~~p~------------------~~~~~~ll~~~~~~~~~~~a~~~~~~m   78 (145)
                      +...-......|++++|.+.|.+-.....  +.++                  ...+..+..++.+.|+++.|...++..
T Consensus        14 ~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~a   93 (179)
T d2ff4a2          14 EKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEAL   93 (179)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHH
Confidence            33444678899999999999998654111  1111                  135677788888889999999988888


Q ss_pred             hhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCC
Q 047113           79 VHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPF  132 (145)
Q Consensus        79 ~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  132 (145)
                      . .  +.|                -+...|..++.+|.+.|+.++|++.|++..
T Consensus        94 l-~--~~P----------------~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~  128 (179)
T d2ff4a2          94 T-F--EHP----------------YREPLWTQLITAYYLSDRQSDALGAYRRVK  128 (179)
T ss_dssp             H-H--HST----------------TCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             H-H--hCC----------------ccHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            8 2  343                266788999999999999999999999864

>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=97.20  E-value=0.00054  Score=42.45  Aligned_cols=110  Identities=13%  Similarity=-0.027  Sum_probs=75.3

Q ss_pred             hhHHHH--HHHHHHcCChHHHHHHHHHhHhhcCCCCc----------HHHHHHHHHHhhccchHHHHHHHHHHhhhhcC-
Q 047113           17 VIWSGM--IASHAIHGQEREALEAFYLVIHCSDGKPN----------NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQ-   83 (145)
Q Consensus        17 ~~~~~l--i~a~~~~g~~~~A~~~~~~m~~~~~~~p~----------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~-   83 (145)
                      .+|..+  ...+.+.|++++|+..|.+-.+-..-.|+          ...|+.+-.++...|+++.|...++....-.. 
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~   87 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR   87 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc
Confidence            467777  45566789999999999996531222222          46788999999999999999998888772110 


Q ss_pred             -cCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCC
Q 047113           84 -LDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDP  136 (145)
Q Consensus        84 -~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  136 (145)
                       ...+......          ...+++.+-.+|...|++++|...|++..++.|
T Consensus        88 ~~~~~~~~~~~----------~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~  131 (156)
T d2hr2a1          88 RGELNQDEGKL----------WISAVYSRALALDGLGRGAEAMPEFKKVVEMIE  131 (156)
T ss_dssp             HCCTTSTHHHH----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             cccccccccch----------hHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence             1111000000          112466788999999999999999998777543

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.18  E-value=0.0011  Score=45.02  Aligned_cols=122  Identities=5%  Similarity=-0.040  Sum_probs=84.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhh---hcC-cCccHH
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHC---SDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVH---DFQ-LDLNLE   89 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~-~~~~~~   89 (145)
                      .|.-....|...|++++|...|.+....   .+-+++ ..+|+.+-.++.+.|+++.|...++....   ..| ......
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  118 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHH
Confidence            5777888888888999999999876431   122222 45788888888999999998888886652   111 122244


Q ss_pred             HHHHHHHHHhcC-----------------------CC-chhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           90 HYGITVDLLATG-----------------------ET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        90 ~~~~li~~~~~~-----------------------~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ++..+...|-..                       .+ -..++..+...|...|++++|...++++.+..+..+
T Consensus       119 ~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~  192 (290)
T d1qqea_         119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNR  192 (290)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCT
T ss_pred             HHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccch
Confidence            455555555322                       11 134688889999999999999999999877665444

>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=97.05  E-value=0.002  Score=38.48  Aligned_cols=77  Identities=12%  Similarity=0.056  Sum_probs=59.8

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcC-CCCc-----HHHHHHHHHHhhccchHHHHH
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSD-GKPN-----NVTFLSILFACSYSGLIEEGI   72 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~-~~p~-----~~~~~~ll~~~~~~~~~~~a~   72 (145)
                      ++|.+.|.+.   .+.+...|..+-.+|.+.|++++|+..+++..+ .. -.+.     ..+|..+-..+...++++.|.
T Consensus        21 ~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~-l~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~   99 (128)
T d1elra_          21 DTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIE-VGRENREDYRQIAKAYARIGNSYFKEEKYKDAI   99 (128)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHH-hCcccHHHHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence            5778888754   345788999999999999999999999999754 11 0111     246677777888889999999


Q ss_pred             HHHHHhh
Q 047113           73 KVFDIMV   79 (145)
Q Consensus        73 ~~~~~m~   79 (145)
                      ..|....
T Consensus       100 ~~~~kal  106 (128)
T d1elra_         100 HFYNKSL  106 (128)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998876

>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=97.03  E-value=0.00014  Score=44.92  Aligned_cols=101  Identities=12%  Similarity=0.033  Sum_probs=64.2

Q ss_pred             HHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc----------hHHHHHHHHHHhhhhcCcCc-cHHHHHH
Q 047113           26 HAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG----------LIEEGIKVFDIMVHDFQLDL-NLEHYGI   93 (145)
Q Consensus        26 ~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~----------~~~~a~~~~~~m~~~~~~~~-~~~~~~~   93 (145)
                      |-+.+.+++|...|+...+   +.| |...+..+-.++...+          .++.|...|+...   .+.| +...|..
T Consensus         7 ~~r~~~fe~A~~~~e~al~---~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl---~l~P~~~~a~~~   80 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYK---SNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEAL---LIDPKKDEAVWC   80 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH---HHCTTCHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHh---hCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHH---HhcchhhHHHhh
Confidence            4566789999999999765   345 6667777777776544          4466777777776   2445 3445555


Q ss_pred             HHHHHhcC---CCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCCCC
Q 047113           94 TVDLLATG---ETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKNDAY  141 (145)
Q Consensus        94 li~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  141 (145)
                      +..+|...   .++..-         ..+++++|...|++..+++|+++.+
T Consensus        81 lG~~y~~~g~~~~~~~~---------~~~~~~~A~~~~~kal~l~P~~~~~  122 (145)
T d1zu2a1          81 IGNAYTSFAFLTPDETE---------AKHNFDLATQFFQQAVDEQPDNTHY  122 (145)
T ss_dssp             HHHHHHHHHHHCCCHHH---------HHHHHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHcccchhhHHH---------HHHhHHHhhhhhhcccccCCCHHHH
Confidence            54444332   111111         1234688999999988899877644

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.02  E-value=0.0041  Score=42.02  Aligned_cols=122  Identities=8%  Similarity=-0.096  Sum_probs=78.4

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhh---cCCCC-cHHHHHHHHHHh-hccchHHHHHHHHHHhhhh---cCcCc-c
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHC---SDGKP-NNVTFLSILFAC-SYSGLIEEGIKVFDIMVHD---FQLDL-N   87 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~---~~~~p-~~~~~~~ll~~~-~~~~~~~~a~~~~~~m~~~---~~~~~-~   87 (145)
                      .+|+.+...|.+.|++++|...|+...+.   .|-.. ...++..+...+ ...|+++.|.+.+.....-   .+-.+ -
T Consensus        78 ~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~  157 (290)
T d1qqea_          78 NTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALS  157 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhh
Confidence            57999999999999999999999875320   22111 234556666666 4469999999999877621   12222 2


Q ss_pred             HHHHHHHHHHHhcC----------------CCch--------hhHHHHHHHHHhccChhHHHHHHccCCCCCCCC
Q 047113           88 LEHYGITVDLLATG----------------ETEP--------YVWGALLGACRIHHNVKIGELVAKDPFHLDPKN  138 (145)
Q Consensus        88 ~~~~~~li~~~~~~----------------~p~~--------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  138 (145)
                      ..++..+...|.+.                .+..        ..+..++..+...|+++.|...+++..+..|..
T Consensus       158 ~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~  232 (290)
T d1qqea_         158 NKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNF  232 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC----
T ss_pred             hhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCc
Confidence            44566667777666                1111        123344556677899999999999999887643

>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=96.79  E-value=0.0064  Score=37.26  Aligned_cols=61  Identities=16%  Similarity=0.111  Sum_probs=54.7

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .+|+.+..+|.+.|++++|++.+....+ .. +.+...|..+..++...|+++.|...|+...
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~-~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al  128 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLK-ID-KNNVKALYKLGVANMYFGFLEEAKENLYKAA  128 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccc-cc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHH
Confidence            4788899999999999999999999876 33 3378899999999999999999999999988

>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=96.79  E-value=0.0023  Score=39.15  Aligned_cols=89  Identities=11%  Similarity=0.017  Sum_probs=61.9

Q ss_pred             CchHHHHhccC---CCCchhhHHHHHHHHHHc----------CChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccc
Q 047113            1 MDDAERIFGGI---IDKNVVIWSGMIASHAIH----------GQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSG   66 (145)
Q Consensus         1 ~~~A~~~f~~m---~~~~~~~~~~li~a~~~~----------g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~   66 (145)
                      +++|...|+..   .+.+...|..+-.++...          +.+++|+..|+...+   +.| +..+|..+-.++...|
T Consensus        13 fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~---l~P~~~~a~~~lG~~y~~~g   89 (145)
T d1zu2a1          13 FEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL---IDPKKDEAVWCIGNAYTSFA   89 (145)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHH---hcchhhHHHhhHHHHHHHcc
Confidence            46788888865   345777888888887754          456889999999876   456 6778888888887655


Q ss_pred             h-----------HHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           67 L-----------IEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        67 ~-----------~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .           ++.|.+.|+...   .+.|+-.+|..-+
T Consensus        90 ~~~~~~~~~~~~~~~A~~~~~kal---~l~P~~~~~~~~L  126 (145)
T d1zu2a1          90 FLTPDETEAKHNFDLATQFFQQAV---DEQPDNTHYLKSL  126 (145)
T ss_dssp             HHCCCHHHHHHHHHHHHHHHHHHH---HHCTTCHHHHHHH
T ss_pred             cchhhHHHHHHhHHHhhhhhhccc---ccCCCHHHHHHHH
Confidence            3           566777777766   4566655544433

>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=96.78  E-value=0.0077  Score=37.35  Aligned_cols=62  Identities=6%  Similarity=-0.046  Sum_probs=55.3

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      +...|+.+-.++.+.|++++|+..|....+   +.| +...|..+-.++...|+++.|.+.|+...
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~---~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al  138 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALE---IDPSNTKALYRRAQGWQGLKEYDQALADLKKAQ  138 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhh---hhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHH
Confidence            455788889999999999999999999866   345 67899999999999999999999999998

>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=96.51  E-value=0.014  Score=36.25  Aligned_cols=60  Identities=12%  Similarity=-0.057  Sum_probs=54.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      .+|+.+-.+|.+.|++++|+..++.... .  .| +...|..+-.++...|+++.|...|+...
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~-~--~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al  123 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALE-L--DSNNEKGLSRRGEAHLAVNDFELARADFQKVL  123 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-H--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhh-c--cccchhhhHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            4688888999999999999999999876 3  46 78899999999999999999999999998

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.42  E-value=0.0073  Score=41.32  Aligned_cols=108  Identities=9%  Similarity=0.030  Sum_probs=62.3

Q ss_pred             cCChHHHHHHHHHhHhhcCCCCcHH-HHHHHHHH----------hhccchHHHHHHHHHHhhhhcCcCc-cHHHHHHHHH
Q 047113           29 HGQEREALEAFYLVIHCSDGKPNNV-TFLSILFA----------CSYSGLIEEGIKVFDIMVHDFQLDL-NLEHYGITVD   96 (145)
Q Consensus        29 ~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~ll~~----------~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~   96 (145)
                      .+..++|++++....+   ..|+.. .|+..-..          ....|.++.+..+++... .  ..| +...|..+..
T Consensus        42 ~~~~~~al~~~~~~l~---~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l-~--~~pk~~~~~~~~~~  115 (334)
T d1dcea1          42 GELDESVLELTSQILG---ANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCL-R--VNPKSYGTWHHRCW  115 (334)
T ss_dssp             TCCSHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH-H--HCTTCHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHH---HCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHH-H--hCCCcHHHHHHhhH
Confidence            3344777777777654   346433 33322211          223445666777777766 2  233 4555555444


Q ss_pred             HHhcC-------------------CCchhhHHHHH-HHHHhccChhHHHHHHccCCCCCCCCCCCc
Q 047113           97 LLATG-------------------ETEPYVWGALL-GACRIHHNVKIGELVAKDPFHLDPKNDAYY  142 (145)
Q Consensus        97 ~~~~~-------------------~p~~~~~~~li-~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  142 (145)
                      ++...                   +++...|...+ ..+...|++++|+..+++..+.+|++...|
T Consensus       116 ~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~  181 (334)
T d1dcea1         116 LLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSW  181 (334)
T ss_dssp             HHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHH
T ss_pred             HHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHH
Confidence            44332                   44555665544 556667888888888888888888766554

>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=96.41  E-value=0.029  Score=37.31  Aligned_cols=114  Identities=11%  Similarity=-0.046  Sum_probs=78.3

Q ss_pred             hHHHHhccCCCC---chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC---cHHHHHHHHHHhhccchHHHHHHHHH
Q 047113            3 DAERIFGGIIDK---NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP---NNVTFLSILFACSYSGLIEEGIKVFD   76 (145)
Q Consensus         3 ~A~~~f~~m~~~---~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p---~~~~~~~ll~~~~~~~~~~~a~~~~~   76 (145)
                      +|..++......   ....+..+...+...|++++|...+..... .....   ....+..+..++...|+++.|...++
T Consensus       197 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  275 (366)
T d1hz4a_         197 RLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAK-PEFANNHFLQGQWRNIARAQILLGEFEPAEIVLE  275 (366)
T ss_dssp             HHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCC-CCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHH-hccccchHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            344445444432   234677888889999999999999988654 22211   24456677888999999999999999


Q ss_pred             Hhhhh---cCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           77 IMVHD---FQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        77 ~m~~~---~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      .....   .+..|+                ....+..+-..|.+.|++++|.+.+++..+
T Consensus       276 ~al~~~~~~~~~~~----------------~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         276 ELNENARSLRLMSD----------------LNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHTTCHHH----------------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcccChH----------------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            87621   122222                234566677888889999999988877544

>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=96.31  E-value=0.023  Score=31.71  Aligned_cols=73  Identities=7%  Similarity=-0.057  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHhHhhc----CCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc-HHHHH
Q 047113           19 WSGMIASHAIHGQEREALEAFYLVIHCS----DGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN-LEHYG   92 (145)
Q Consensus        19 ~~~li~a~~~~g~~~~A~~~~~~m~~~~----~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~   92 (145)
                      +-.+-..+.+.|++++|...|++..+..    ...++ ..+++.+-.++.+.|++++|...+++..   .+.|+ ...++
T Consensus         8 c~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL---~l~P~~~~a~~   84 (95)
T d1tjca_           8 SFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLL---ELDPEHQRANG   84 (95)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH---HHCTTCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHH---HhCcCCHHHHH
Confidence            3467788899999999999998854311    11222 5688999999999999999999999998   34564 44444


Q ss_pred             HH
Q 047113           93 IT   94 (145)
Q Consensus        93 ~l   94 (145)
                      .+
T Consensus        85 Nl   86 (95)
T d1tjca_          85 NL   86 (95)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=96.13  E-value=0.037  Score=34.08  Aligned_cols=66  Identities=11%  Similarity=0.021  Sum_probs=55.7

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCcc
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLN   87 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~   87 (145)
                      ..|+.+-.+|.+.|++++|+..+..... .. +.+...|..+-.++...|+++.|...|.... .  +.|+
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~-l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al-~--l~P~  130 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALG-LD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVL-E--VNPQ  130 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--SCTT
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhh-cc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHH-H--hCCC
Confidence            4577788889999999999999999876 33 3478899999999999999999999999998 3  4554

>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=96.05  E-value=0.0012  Score=48.52  Aligned_cols=99  Identities=6%  Similarity=-0.118  Sum_probs=42.9

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHH
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGI   93 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~   93 (145)
                      +...|+.+-..+.+.|+.++|...+..-..     ++ ...+..+-+.+...|+++.|...+.+..   .+.|+      
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~-----~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~---~l~P~------  184 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCS-----YICQHCLVHLGDIARYRNQTSQAESYYRHAA---QLVPS------  184 (497)
T ss_dssp             ------------------------CCHHHH-----HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH---HHCTT------
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhC-----CCHHHHHHHHHHHHHHcccHHHHHHHHHHHH---HHCCC------
Confidence            444566666666667777777666655433     22 2456666777777777777777777766   23442      


Q ss_pred             HHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCC
Q 047113           94 TVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPK  137 (145)
Q Consensus        94 li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  137 (145)
                                +...|+.|-..+...|+..+|...|.+...+.|+
T Consensus       185 ----------~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~  218 (497)
T d1ya0a1         185 ----------NGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFP  218 (497)
T ss_dssp             ----------BSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBC
T ss_pred             ----------chHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC
Confidence                      3445555555555555665555555555544443

>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=96.00  E-value=0.033  Score=37.06  Aligned_cols=107  Identities=10%  Similarity=-0.019  Sum_probs=56.5

Q ss_pred             HHHHHcCChHHHHHHHHHhHhhcCCCCc------HHHHHHHHHHhhccchHHHHHHHHHHhhhhc---CcCc-cHHHHHH
Q 047113           24 ASHAIHGQEREALEAFYLVIHCSDGKPN------NVTFLSILFACSYSGLIEEGIKVFDIMVHDF---QLDL-NLEHYGI   93 (145)
Q Consensus        24 ~a~~~~g~~~~A~~~~~~m~~~~~~~p~------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~-~~~~~~~   93 (145)
                      ..+...|++++|..+|++... .  .|+      ...++.+-..+...|+++.|...++......   +-.+ ....+..
T Consensus        20 ~~~~~~g~~~~A~~~~~~aL~-~--~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   96 (366)
T d1hz4a_          20 QVAINDGNPDEAERLAKLALE-E--LPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQ   96 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH-T--CCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHh-h--CcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHH
Confidence            345567777777777776543 1  222      2345555666677777777777777665211   1111 1222222


Q ss_pred             HHHHHhcC------------------------CCc-hhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           94 TVDLLATG------------------------ETE-PYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        94 li~~~~~~------------------------~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      +...|...                        .+. ...+..+-..+...|+++.+...+.....
T Consensus        97 ~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~  161 (366)
T d1hz4a_          97 QSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIE  161 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHH
Confidence            32333222                        111 12444555667777888888777776555

>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=95.58  E-value=0.055  Score=39.31  Aligned_cols=80  Identities=10%  Similarity=-0.067  Sum_probs=68.2

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCC-cHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           17 VIWSGMIASHAIHGQEREALEAFYLVIHCSDGKP-NNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        17 ~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      .++..|-+.+...|++++|...|.+..+   +.| +..+|+.+-..+...|+...|...|.+.. ... .|-...+..|.
T Consensus       153 ~~~~~LG~l~~~~~~~~~A~~~y~~A~~---l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral-~~~-~~~~~a~~nL~  227 (497)
T d1ya0a1         153 HCLVHLGDIARYRNQTSQAESYYRHAAQ---LVPSNGQPYNQLAILASSKGDHLTTIFYYCRSI-AVK-FPFPAASTNLQ  227 (497)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHH-SSS-BCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHH---HCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHH-hCC-CCCHHHHHHHH
Confidence            4688889999999999999999999765   456 56799999999999999999999999888 433 56788899999


Q ss_pred             HHHhcC
Q 047113           96 DLLATG  101 (145)
Q Consensus        96 ~~~~~~  101 (145)
                      ..|.+.
T Consensus       228 ~~~~~~  233 (497)
T d1ya0a1         228 KALSKA  233 (497)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            888766

>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=95.42  E-value=0.032  Score=31.77  Aligned_cols=63  Identities=13%  Similarity=0.179  Sum_probs=50.7

Q ss_pred             ChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHH
Q 047113           31 QEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVD   96 (145)
Q Consensus        31 ~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~   96 (145)
                      |.=++.+-++.+-. .++.|+.....+.+.+|.+-+++..|.++|+..+.+.|  ++-..|..+++
T Consensus        21 D~we~rrgmN~l~~-~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~--~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVG-YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTT-SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CcHHHHHHHHH
Confidence            34467777777777 88999999999999999999999999999999984443  34557776664

>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=95.40  E-value=0.0097  Score=33.41  Aligned_cols=72  Identities=11%  Similarity=-0.006  Sum_probs=53.5

Q ss_pred             HHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCC-chhhHHHHHHHHHhccChhHHHHHHccCCCCC
Q 047113           57 SILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGET-EPYVWGALLGACRIHHNVKIGELVAKDPFHLD  135 (145)
Q Consensus        57 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  135 (145)
                      -+-..+-+.|+++.|...|++......-.+.             ..+ ...+++.|-.+|.+.|++++|...+++..+++
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~-------------~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEI-------------STIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCC-------------CSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhc-------------cCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            4556678899999999999887722111110             012 23567888999999999999999999999999


Q ss_pred             CCCCCC
Q 047113          136 PKNDAY  141 (145)
Q Consensus       136 ~~~~~~  141 (145)
                      |+++..
T Consensus        77 P~~~~a   82 (95)
T d1tjca_          77 PEHQRA   82 (95)
T ss_dssp             TTCHHH
T ss_pred             cCCHHH
Confidence            987654

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=95.37  E-value=0.098  Score=31.59  Aligned_cols=64  Identities=19%  Similarity=0.104  Sum_probs=49.9

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhh----cCCCCc-----HHHHHHHHHHhhccchHHHHHHHHHHhh
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHC----SDGKPN-----NVTFLSILFACSYSGLIEEGIKVFDIMV   79 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~----~~~~p~-----~~~~~~ll~~~~~~~~~~~a~~~~~~m~   79 (145)
                      ..+|+.+-.+|.+.|++++|...+++....    ....++     ...++.+-.++...|++++|...|++..
T Consensus        55 a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          55 AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            367999999999999999999999886430    112222     2256777889999999999999999876

>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=92.96  E-value=0.12  Score=34.44  Aligned_cols=59  Identities=17%  Similarity=0.075  Sum_probs=43.7

Q ss_pred             chHHHHhccC---CCCchhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCc-HHHHHHHHHHhh
Q 047113            2 DDAERIFGGI---IDKNVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPN-NVTFLSILFACS   63 (145)
Q Consensus         2 ~~A~~~f~~m---~~~~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~ll~~~~   63 (145)
                      ++|.+.+++.   .+.|...+..+...+++.|++++|...|+...+   +.|+ ...+..+-....
T Consensus        13 ~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~---l~P~~~~~~~~l~~ll~   75 (264)
T d1zbpa1          13 QQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIK---LFPEYLPGASQLRHLVK   75 (264)
T ss_dssp             HHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHH
Confidence            5677777754   345788999999999999999999999999866   4564 334444444433

>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=92.35  E-value=0.44  Score=32.85  Aligned_cols=18  Identities=6%  Similarity=-0.110  Sum_probs=10.7

Q ss_pred             CCchhhHHHHHHHHHhcc
Q 047113          102 ETEPYVWGALLGACRIHH  119 (145)
Q Consensus       102 ~p~~~~~~~li~~~~~~g  119 (145)
                      .++...++.++..|++.+
T Consensus       130 ~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_         130 RAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             TCCHHHHHHHHHHHHTTC
T ss_pred             ccchHHHHHHHHHHHHhC
Confidence            445556666666666653

>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=89.48  E-value=2.2  Score=29.20  Aligned_cols=110  Identities=10%  Similarity=-0.054  Sum_probs=66.7

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcCccHHHHHHHH
Q 047113           16 VVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLDLNLEHYGITV   95 (145)
Q Consensus        16 ~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li   95 (145)
                      ..+|..+..++.+.....-|     ++.. .....+......++..+-..|.++....+++... .. -..+...++-++
T Consensus        69 ~~~~k~~~~~l~~~~e~~la-----~i~~-~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~-~~-~~~~~~~~~~L~  140 (336)
T d1b89a_          69 TRTWKEVCFACVDGKEFRLA-----QMCG-LHIVVHADELEELINYYQDRGYFEELITMLEAAL-GL-ERAHMGMFTELA  140 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHH-----HHTT-TTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TS-TTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHH-----HHHH-HHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHH-cC-CccchHHHHHHH
Confidence            34555555555555444332     1112 2334455666788888999999988888888766 21 245677889999


Q ss_pred             HHHhcC-----------CCchhhHHHHHHHHHhccChhHHHHHHccCCC
Q 047113           96 DLLATG-----------ETEPYVWGALLGACRIHHNVKIGELVAKDPFH  133 (145)
Q Consensus        96 ~~~~~~-----------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  133 (145)
                      ..|++.           ..+....-.++..|...+-++++.-++.++..
T Consensus       141 ~lyak~~~~kl~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~  189 (336)
T d1b89a_         141 ILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEE  189 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             HHHHHhChHHHHHHHHhccccCCHHHHHHHHHHcCChHHHHHHHHhcCC
Confidence            999998           12223334455666666666666655555443

>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=87.80  E-value=0.43  Score=28.09  Aligned_cols=58  Identities=10%  Similarity=0.001  Sum_probs=36.9

Q ss_pred             ccchHHHHHHHHHHhhhhcCcCccHHHHHHHHHHHhcCCCchhhHHHHHHHHHhccChhHHHHHHccCCCCCCCCC
Q 047113           64 YSGLIEEGIKVFDIMVHDFQLDLNLEHYGITVDLLATGETEPYVWGALLGACRIHHNVKIGELVAKDPFHLDPKND  139 (145)
Q Consensus        64 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  139 (145)
                      ...+++.|..+++... +.+  |.-               ....+-.|--+|.+.|++++|++.++.+.+++|++.
T Consensus        50 ~~~d~~~gI~lLe~~~-~~~--p~~---------------~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~n~  107 (124)
T d2pqrb1          50 DVNDERLGVKILTDIY-KEA--ESR---------------RRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNK  107 (124)
T ss_dssp             CHHHHHHHHHHHHHHH-HHC--GGG---------------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCH
T ss_pred             cHHHHHHHHHHHHHHH-hcC--chh---------------HHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCCcH
Confidence            4456777888887776 322  210               112333344567788888888888888888888654

>d2nsza1 a.118.1.14 (A:322-450) Programmed cell death 4, PDCD4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Programmed cell death 4, PDCD4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.28  E-value=2.3  Score=24.82  Aligned_cols=101  Identities=7%  Similarity=-0.037  Sum_probs=59.6

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchH--HHHHHHHHHhhhhcCcCccHHHHHH--
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLI--EEGIKVFDIMVHDFQLDLNLEHYGI--   93 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~--~~a~~~~~~m~~~~~~~~~~~~~~~--   93 (145)
                      ....+|.-|..+|+.++|...++++.. .... ....+..+..+.-+.+.-  +....++..+. ..|+-+....-..  
T Consensus         9 k~~~ll~EY~~~~D~~Ea~~~l~eL~~-p~~~-~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~-~~~~is~~~i~~Gf~   85 (129)
T d2nsza1           9 EIDMLLKEYLLSGDISEAEHCLKELEV-PHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLW-KSSTITIDQMKRGYE   85 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTC-GGGH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHH-HTTCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCC-chhh-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHH
Confidence            467899999999999999999999864 2223 233444444444444433  34677899998 6665554333333  


Q ss_pred             -HHHHHhcC---CCchhhHHHH-HHHHHhccCh
Q 047113           94 -TVDLLATG---ETEPYVWGAL-LGACRIHHNV  121 (145)
Q Consensus        94 -li~~~~~~---~p~~~~~~~l-i~~~~~~g~~  121 (145)
                       +++..-..   .|+...+-.- +.-+...|-+
T Consensus        86 ~~l~~l~Dl~lDvP~a~~~l~~fi~rav~d~~l  118 (129)
T d2nsza1          86 RIYNEIPDINLDVPHSYSVLERFVEECFQAGII  118 (129)
T ss_dssp             HHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTCS
T ss_pred             HHHhhCcHHhhccccHHHHHHHHHHHHHHcCCC
Confidence             33322222   7777654443 3333444443

>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=85.23  E-value=2.4  Score=25.17  Aligned_cols=68  Identities=9%  Similarity=-0.028  Sum_probs=47.1

Q ss_pred             chhhHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccchHHHHHHHHHHhhhhcCcC
Q 047113           15 NVVIWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGLIEEGIKVFDIMVHDFQLD   85 (145)
Q Consensus        15 ~~~~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~   85 (145)
                      +..-.+-.++...+.|+-++-.++++.+.+ .+ +|++...-.+-.+|.+-|...++.+++.+.. +.|+.
T Consensus        85 ~se~vdlALd~lv~~~kkd~Ld~i~~~l~k-n~-~i~~~~llkia~A~kkig~~re~nell~~AC-e~G~K  152 (161)
T d1wy6a1          85 LNEHVNKALDILVIQGKRDKLEEIGREILK-NN-EVSASILVAIANALRRVGDERDATTLLIEAC-KKGEK  152 (161)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HTTCH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHH-HHhHH
Confidence            334466677777888888888888777544 33 5666666777778888888888888877776 55654

>d1ug3a1 a.118.1.14 (A:1235-1427) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Eukaryotic initiation factor eIF4G
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.06  E-value=2.1  Score=26.81  Aligned_cols=64  Identities=6%  Similarity=-0.190  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHhHhhcCCCCcHHHHHHHHHHhhccch--HHHHHHHHHHhhhhcCcC
Q 047113           18 IWSGMIASHAIHGQEREALEAFYLVIHCSDGKPNNVTFLSILFACSYSGL--IEEGIKVFDIMVHDFQLD   85 (145)
Q Consensus        18 ~~~~li~a~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~ll~~~~~~~~--~~~a~~~~~~m~~~~~~~   85 (145)
                      ....+|.-|...|+.++|...++++.. ..+.|.. . ..++......++  -+....++..+. +.|+-
T Consensus        12 k~~~il~Ey~~~~D~~Ea~~~l~el~~-p~~~~~~-V-~~~i~~~le~~~~~re~~~~Ll~~L~-~~~~i   77 (193)
T d1ug3a1          12 KSKAIIEEYLHLNDMKEAVQCVQELAS-PSLLFIF-V-RHGVESTLERSAIAREHMGQLLHQLL-CAGHL   77 (193)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHTTCC-GGGHHHH-H-HHHHHHHTTTCHHHHHHHHHHHHHHH-HTTSS
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCC-chhHHHH-H-HHHHHHHHcCCHHHHHHHHHHHHHHH-HCCCC
Confidence            467889999999999999999999864 3333222 2 223333333333  345666677776 45544