Citrus Sinensis ID: 025225

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250------
Protein Sequence
MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEEIFGKL
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHccccccHHHHHHHcccccccccHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHcccccHHHHHHHHHcccccccccccccHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHccccHHHHHHHHHHHHccccccccHHHcccccccccccccccccccccccccccccHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHcccccEEEEcccccccccc
Coil and Loop (DISEMBL)
matrlfsrskipILASIVLQnltknpsknfsflafkpkspivdfvahepilglrqyhdgrprgslwrgkkligkEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIrkqdwyqpdaYIYKDLIIALARTGKMNEAMQVWESMrkedlfpdsqtYTEVIRGflkdgspadaMNIYedmikspdppeelpFRILLKgllphpllrskVKKDFEelfpekhaydppeeifgkl
Flexible Loop (DISEMBL)
matrlfsrskipilASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILglrqyhdgrprgslwrgkkligkEALFVILGLkrfkddeeKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELfpekhaydppeeifgkl
Low Complexity Region (SEG)
MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIllkgllphpllRSKVKKDFEELFPEKHAYDPPEEIFGKL
Disordered region (IsUnstruct)
*********KIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG*****MNIY************LPFRILLKGLLPHPLLRSKV************************
Disordered Region (DISOPRED)
********SKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEEIFGKL
Disordered Region (DISEMBL)
MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEEIFGKL
Disordered Region (DISPRO)
****LFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEEIFGKL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEEIFGKL
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	256	2.2.26 [Sep-21-2011]
Q9STF9	257	Pentatricopeptide repeat-	yes	no	0.992	0.988	0.699	1e-102
Q1PFH7	196	Pentatricopeptide repeat-	no	no	0.707	0.923	0.458	7e-45
Q9SI78	485	Pentatricopeptide repeat-	no	no	0.390	0.206	0.316	5e-10
Q9LFC5	729	Pentatricopeptide repeat-	no	no	0.519	0.182	0.242	3e-09
Q9SUD8	704	Pentatricopeptide repeat-	no	no	0.308	0.112	0.383	4e-09
Q76C99	791	Protein Rf1, mitochondria	N/A	no	0.324	0.104	0.380	5e-09
Q9SXD8	634	Pentatricopeptide repeat-	no	no	0.390	0.157	0.267	1e-08
Q0WVK7	741	Pentatricopeptide repeat-	no	no	0.410	0.141	0.320	2e-08
Q3E9F0	506	Pentatricopeptide repeat-	no	no	0.406	0.205	0.295	2e-08
Q9LN22	537	Pentatricopeptide repeat-	no	no	0.417	0.199	0.275	2e-08

>sp|Q9STF9|PP266_ARATH Pentatricopeptide repeat-containing protein At3g46870 OS=Arabidopsis thaliana GN=At3g46870 PE=2 SV=1

 Score =  371 bits (952), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/256 (69%), Positives = 217/256 (84%), Gaps = 2/256 (0%)

Query: 2   ATRLFSRSKIPILASIVLQNLTKNPS-KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGR 60
           A R+ SR K P  ASI  QN+T+NPS    SF   KPK+ +         + + ++HDGR
Sbjct: 3   AIRVCSR-KFPTFASIFFQNITRNPSIHRISFSNLKPKTLLHPIPPKPFTVFVSRFHDGR 61

Query: 61  PRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQE 120
           PRG LWRGKKLIGKEALFVILGLKR K+D+EKL KFIKTHV RLLK+D++AV+ ELERQE
Sbjct: 62  PRGPLWRGKKLIGKEALFVILGLKRLKEDDEKLDKFIKTHVFRLLKLDMLAVIGELERQE 121

Query: 121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY 180
           ET LA+K+F++I+KQ+WYQPD ++YKDLI++LA++ +M+EAM +WE M+KE+LFPDSQTY
Sbjct: 122 ETALAIKMFEVIQKQEWYQPDVFMYKDLIVSLAKSKRMDEAMALWEKMKKENLFPDSQTY 181

Query: 181 TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELF 240
           TEVIRGFL+DG PADAMN+YEDM+KSPDPPEELPFR+LLKGLLPHPLLR+KVKKDFEELF
Sbjct: 182 TEVIRGFLRDGCPADAMNVYEDMLKSPDPPEELPFRVLLKGLLPHPLLRNKVKKDFEELF 241

Query: 241 PEKHAYDPPEEIFGKL 256
           PEKHAYDPPEEIFG+ 
Sbjct: 242 PEKHAYDPPEEIFGRC 257

Arabidopsis thaliana (taxid: 3702)

>sp|Q1PFH7|PPR89_ARATH Pentatricopeptide repeat-containing protein At1g62350 OS=Arabidopsis thaliana GN=At1g62350 PE=2 SV=1

 Score =  180 bits (457), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 83/181 (45%), Positives = 127/181 (70%)

Query: 72  IGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDI 131
           + KE L     LKR +    +L +FI +HV RLLK D+V+VL E +RQ +  L +K++++
Sbjct: 1   MSKEGLIAAKELKRLQTQSVRLDRFIGSHVSRLLKSDLVSVLAEFQRQNQVFLCMKLYEV 60

Query: 132 IRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG 191
           +R++ WY+PD + Y+D+++ LAR  K++E  +VWE ++KE++  D  T+ +++RGFL + 
Sbjct: 61  VRREIWYRPDMFFYRDMLMMLARNKKVDETKKVWEDLKKEEVLFDQHTFGDLVRGFLDNE 120

Query: 192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEE 251
            P +AM +Y +M +SPD P  LPFR++LKGL+P+P LR KVK DF ELFP    YDPPE+
Sbjct: 121 LPLEAMRLYGEMRESPDRPLSLPFRVILKGLVPYPELREKVKDDFLELFPGMIVYDPPED 180

Query: 252 I 252
           I
Sbjct: 181 I 181

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SI78|PPR93_ARATH Pentatricopeptide repeat-containing protein At1g62720 OS=Arabidopsis thaliana GN=At1g62720 PE=2 SV=1

 Score = 65.1 bits (157), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 58/101 (57%), Gaps = 1/101 (0%)

Query: 125 AVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVI 184
           AV++FD + ++D  + DA  Y  L+  L  +G+ ++A ++   M   D+ P+  T+T VI
Sbjct: 193 AVELFDRM-ERDGVRADAVTYNSLVAGLCCSGRWSDAARLMRDMVMRDIVPNVITFTAVI 251

Query: 185 RGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH 225
             F+K+G  ++AM +YE+M +    P+   +  L+ GL  H
Sbjct: 252 DVFVKEGKFSEAMKLYEEMTRRCVDPDVFTYNSLINGLCMH 292

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LFC5|PP360_ARATH Pentatricopeptide repeat-containing protein At5g01110 OS=Arabidopsis thaliana GN=At5g01110 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/140 (24%), Positives = 74/140 (52%), Gaps = 7/140 (5%)

Query: 111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK 170
           ++L+E  ++ + +   K+F  +R +D   PD   +  ++    R+G +++A+  + S+++
Sbjct: 345 SLLMEACKKGDVVETEKVFSDMRSRDVV-PDLVCFSSMMSLFTRSGNLDKALMYFNSVKE 403

Query: 171 EDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS 230
             L PD+  YT +I+G+ + G  + AMN+  +M++     + + +  +L GL    +L  
Sbjct: 404 AGLIPDNVIYTILIQGYCRKGMISVAMNLRNEMLQQGCAMDVVTYNTILHGLCKRKML-G 462

Query: 231 KVKKDFEE-----LFPEKHA 245
           +  K F E     LFP+ + 
Sbjct: 463 EADKLFNEMTERALFPDSYT 482

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SUD8|PP340_ARATH Pentatricopeptide repeat-containing protein At4g28010 OS=Arabidopsis thaliana GN=At4g28010 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 46/86 (53%)

Query: 139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMN 198
           +P+ Y Y  LI  L   GK  EA+Q+   M ++D  P++ TY  +I    KDG  ADA+ 
Sbjct: 314 RPNVYTYTGLIDGLCGVGKTKEALQLLNLMIEKDEEPNAVTYNIIINKLCKDGLVADAVE 373

Query: 199 IYEDMIKSPDPPEELPFRILLKGLLP 224
           I E M K    P+ + + ILL GL  
Sbjct: 374 IVELMKKRRTRPDNITYNILLGGLCA 399

Arabidopsis thaliana (taxid: 3702)

>sp|Q76C99|RF1_ORYSI Protein Rf1, mitochondrial OS=Oryza sativa subsp. indica GN=Rf1 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 32/84 (38%), Positives = 47/84 (55%)

Query: 139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMN 198
            PD Y++  LI A A+ GK+++AM V+  MR++ L P++ TY  VI    K G   DAM 
Sbjct: 368 HPDHYVFSILICAYAKQGKVDQAMLVFSKMRQQGLNPNAVTYGAVIGILCKSGRVEDAML 427

Query: 199 IYEDMIKSPDPPEELPFRILLKGL 222
            +E MI     P  + +  L+ GL
Sbjct: 428 YFEQMIDEGLSPGNIVYNSLIHGL 451

Reduces the expression of the cytoplasmic male sterility (CMS)-associated mitochondrial gene ORF79, encoding a cytotoxic peptide. Can restore male fertility by blocking ORF79 production via endonucleolytic cleavage of dicistronic ATP6/ORF79 mRNA. Promotes the editing of ATP6 mRNAs independently of its cleavage function.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q9SXD8|PPR90_ARATH Pentatricopeptide repeat-containing protein At1g62590 OS=Arabidopsis thaliana GN=At1g62590 PE=2 SV=1

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/101 (26%), Positives = 53/101 (52%), Gaps = 1/101 (0%)

Query: 125 AVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVI 184
           A ++F+ +  +D + PD   Y  LI    ++ ++ +  +++  M    L  D+ TYT +I
Sbjct: 384 AKQMFEFMVSKDCF-PDVVTYNTLIKGFCKSKRVEDGTELFREMSHRGLVGDTVTYTTLI 442

Query: 185 RGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH 225
           +G   DG   +A  +++ M+    PP+ + + ILL GL  +
Sbjct: 443 QGLFHDGDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNN 483

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WVK7|PPR12_ARATH Pentatricopeptide repeat-containing protein At1g05670, mitochondrial OS=Arabidopsis thaliana GN=At1g05670 PE=2 SV=1

 Score = 60.1 bits (144), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 52/106 (49%), Gaps = 1/106 (0%)

Query: 125 AVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVI 184
           A K F  +  +D   PD   Y  +I    + G M EA +++  M  + L PDS T+TE+I
Sbjct: 370 ASKFFYEMHSRD-ITPDVLTYTAIISGFCQIGDMVEAGKLFHEMFCKGLEPDSVTFTELI 428

Query: 185 RGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS 230
            G+ K G   DA  ++  MI++   P  + +  L+ GL     L S
Sbjct: 429 NGYCKAGHMKDAFRVHNHMIQAGCSPNVVTYTTLIDGLCKEGDLDS 474

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E9F0|PP392_ARATH Pentatricopeptide repeat-containing protein At5g18475 OS=Arabidopsis thaliana GN=At5g18475 PE=2 SV=1

 Score = 60.1 bits (144), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/105 (29%), Positives = 55/105 (52%), Gaps = 1/105 (0%)

Query: 118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS 177
           R  E   A KI D ++K +   P+ Y Y  L+    + GK+ EA Q ++ ++K  L  D+
Sbjct: 280 RAGEVERAKKILDFMKK-NGCNPNVYNYSALMNGFCKVGKIQEAKQTFDEVKKTGLKLDT 338

Query: 178 QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL 222
             YT ++  F ++G   +AM +  +M  S    + L + ++L+GL
Sbjct: 339 VGYTTLMNCFCRNGETDEAMKLLGEMKASRCRADTLTYNVILRGL 383

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LN22|PPR54_ARATH Pentatricopeptide repeat-containing protein At1g20300, mitochondrial OS=Arabidopsis thaliana GN=At1g20300 PE=2 SV=1

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 58/109 (53%), Gaps = 2/109 (1%)

Query: 112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE 171
           V+  L R+     A   FD ++  D ++PD  +Y +L+    R G+++EA +V++ M+  
Sbjct: 227 VISNLSRKRRASEAQSFFDSLK--DRFEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLA 284

Query: 172 DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLK 220
            + P+  TY+ VI    + G  + A +++ DM+ S   P  + F  L++
Sbjct: 285 GIEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMR 333

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	256
225434780	252	PREDICTED: pentatricopeptide repeat-cont	0.976	0.992	0.748	1e-107
225434377	252	PREDICTED: pentatricopeptide repeat-cont	0.976	0.992	0.736	1e-106
297815852	257	pentatricopeptide repeat-containing prot	0.992	0.988	0.714	1e-103
255552422	258	conserved hypothetical protein [Ricinus	0.960	0.953	0.719	1e-101
449455076	255	PREDICTED: pentatricopeptide repeat-cont	0.980	0.984	0.710	1e-100
15232674	257	pentatricopeptide repeat-containing prot	0.992	0.988	0.699	1e-100
224106373	257	predicted protein [Populus trichocarpa]	0.988	0.984	0.730	1e-100
356538964	255	PREDICTED: pentatricopeptide repeat-cont	0.976	0.980	0.684	7e-95
357122492	246	PREDICTED: pentatricopeptide repeat-cont	0.785	0.817	0.756	5e-85
326512702	251	predicted protein [Hordeum vulgare subsp	0.785	0.800	0.746	8e-84

>gi|225434780|ref|XP_002281924.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870 isoform 1 [Vitis vinifera] gi|359478900|ref|XP_003632183.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870 isoform 2 [Vitis vinifera] gi|297745987|emb|CBI16043.3| unnamed protein product [Vitis vinifera]

 Score =  392 bits (1007), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 190/254 (74%), Positives = 221/254 (87%), Gaps = 4/254 (1%)

Query: 1   MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGR 60
           MA R FSRSKIPI ++ +LQNL K P K  +   F    P+++  +++P+LG + YHDGR
Sbjct: 1   MAIRAFSRSKIPIFSAKILQNLIKAPIKESTRFQF----PVLEVGSYKPLLGSKLYHDGR 56

Query: 61  PRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQE 120
           PRG LWRGKKLIGKEALFVILGLKRFKDDEE L+KFIK+HVLRLLKMD+VAVL ELERQE
Sbjct: 57  PRGPLWRGKKLIGKEALFVILGLKRFKDDEENLRKFIKSHVLRLLKMDMVAVLTELERQE 116

Query: 121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY 180
           E  LAV++F +IRKQDWY+PD Y+YKDLIIALA+  KM++AMQ+WESMRKEDLFPD QTY
Sbjct: 117 EVSLAVEVFRVIRKQDWYKPDVYLYKDLIIALAKCKKMDDAMQLWESMRKEDLFPDYQTY 176

Query: 181 TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELF 240
           TEVIRGFL+ GSPADAMNIYEDM KSPDPPEELPFRILLKGLLPHPLLR++VK+DFEE+F
Sbjct: 177 TEVIRGFLRYGSPADAMNIYEDMKKSPDPPEELPFRILLKGLLPHPLLRNRVKQDFEEIF 236

Query: 241 PEKHAYDPPEEIFG 254
           P++H YDPPEEIFG
Sbjct: 237 PDRHVYDPPEEIFG 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434377|ref|XP_002276778.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870 [Vitis vinifera] gi|297745785|emb|CBI15841.3| unnamed protein product [Vitis vinifera]

 Score =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 187/254 (73%), Positives = 221/254 (87%), Gaps = 4/254 (1%)

Query: 1   MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGR 60
           MA R FSRSKIPI ++ +LQ+L K+P K  +   F    P+++  +++P+ GL+ YHDGR
Sbjct: 1   MAIRAFSRSKIPIFSAKILQSLIKSPIKESTKFQF----PVLEVASNKPLFGLKHYHDGR 56

Query: 61  PRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQE 120
           PRG LWRGKKLIGKEALFVILGLKRFKDDEEKL+KFIK+HVLRLLKMD++AVL ELERQE
Sbjct: 57  PRGPLWRGKKLIGKEALFVILGLKRFKDDEEKLRKFIKSHVLRLLKMDMIAVLTELERQE 116

Query: 121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY 180
           E  LAV++F + +KQDWY+PD Y+YKDLIIALA+  KM+ AMQ+WESMRKEDLFPD QTY
Sbjct: 117 EVTLAVEVFRVFQKQDWYKPDVYLYKDLIIALAKCKKMDNAMQLWESMRKEDLFPDYQTY 176

Query: 181 TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELF 240
           TEVIRGFL+ GSPADAMNIYEDM KSPDPPEELPFRILLKGLLPHPLLR++VK+DFEE+F
Sbjct: 177 TEVIRGFLRHGSPADAMNIYEDMKKSPDPPEELPFRILLKGLLPHPLLRNRVKQDFEEIF 236

Query: 241 PEKHAYDPPEEIFG 254
           P++H YDPPEEIFG
Sbjct: 237 PDRHVYDPPEEIFG 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297815852|ref|XP_002875809.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297321647|gb|EFH52068.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 183/256 (71%), Positives = 220/256 (85%), Gaps = 2/256 (0%)

Query: 2   ATRLFSRSKIPILASIVLQNLTKNPS-KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGR 60
           A R+FSR K+P  ASI  QNLT+NPS    SF   KPK+ +         + + ++HDGR
Sbjct: 3   AIRVFSR-KLPTFASIFFQNLTRNPSIHRISFSNLKPKTLLHPIPPKPFTVFVSRFHDGR 61

Query: 61  PRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQE 120
           PRG LWRGKKLIGKEALFVILGLKR KDD+EKLQKFIKTHV RLLK+D++AV+ ELERQE
Sbjct: 62  PRGPLWRGKKLIGKEALFVILGLKRLKDDDEKLQKFIKTHVFRLLKLDMLAVIGELERQE 121

Query: 121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY 180
           ET LA+K+F++I+KQ+WYQPD ++YKDLI++LA++ +M+EAM +WE M+KE+LFPDSQTY
Sbjct: 122 ETALAIKMFEVIQKQEWYQPDVFMYKDLIVSLAKSKRMDEAMALWEKMKKENLFPDSQTY 181

Query: 181 TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELF 240
           TEVIRGFL+DG PADAMN+YEDM+KSPDPPEELPFR+LLKGLLPHPLLR+KVKKDFEELF
Sbjct: 182 TEVIRGFLRDGCPADAMNVYEDMLKSPDPPEELPFRVLLKGLLPHPLLRNKVKKDFEELF 241

Query: 241 PEKHAYDPPEEIFGKL 256
           PEKHAYDPPEEIFG+ 
Sbjct: 242 PEKHAYDPPEEIFGRC 257

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552422|ref|XP_002517255.1| conserved hypothetical protein [Ricinus communis] gi|223543626|gb|EEF45155.1| conserved hypothetical protein [Ricinus communis]

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 185/257 (71%), Positives = 210/257 (81%), Gaps = 11/257 (4%)

Query: 6   FSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKS-PIVDFV-------AHEPILGLRQYH 57
           F RS+I  L+ ++LQNLT  P K        P S  + D         +H    GLRQYH
Sbjct: 3   FPRSRIAKLSVVLLQNLTNKPIKQ---TQLPPNSQALFDLNILNKHNHSHNSFSGLRQYH 59

Query: 58  DGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELE 117
           DGRPRG LWRGKKLIGKEALFVILGLKRFKD+EEKL KFIKTHVLRLLKMD++AVL ELE
Sbjct: 60  DGRPRGPLWRGKKLIGKEALFVILGLKRFKDEEEKLDKFIKTHVLRLLKMDMIAVLTELE 119

Query: 118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS 177
           RQEE  LA K+F II+KQDWY PD Y+YKDLIIAL R+GKM++AM++WE+MR E+LFPDS
Sbjct: 120 RQEEVSLATKVFQIIQKQDWYNPDVYLYKDLIIALTRSGKMDQAMKLWEAMRSENLFPDS 179

Query: 178 QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFE 237
           Q YTE+IRGFL+DGSP DAMNIYEDM KSPDPPEELPFRILLKGLLPHPLLR++VK+D+E
Sbjct: 180 QMYTELIRGFLRDGSPGDAMNIYEDMKKSPDPPEELPFRILLKGLLPHPLLRNRVKQDYE 239

Query: 238 ELFPEKHAYDPPEEIFG 254
           ELFPEKH YDPPEEIFG
Sbjct: 240 ELFPEKHVYDPPEEIFG 256

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455076|ref|XP_004145279.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870-like [Cucumis sativus] gi|449475090|ref|XP_004154371.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870-like [Cucumis sativus] gi|449508514|ref|XP_004163333.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870-like [Cucumis sativus]

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 182/256 (71%), Positives = 216/256 (84%), Gaps = 5/256 (1%)

Query: 1   MATRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFV--AHEPILGLRQYHD 58
           MA R FSRSK+P+ AS+ LQ LT+ P ++   +    KS I DF   +  PI G R YHD
Sbjct: 1   MAIRWFSRSKLPVFASVFLQGLTRRPIRD---VPLPVKSTITDFQPDSRRPIWGFRLYHD 57

Query: 59  GRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELER 118
           GRPRG LWR +K IGKEALFVI GLKRFK+DEEK +KF+K+HV RLLK+D+VAVL ELER
Sbjct: 58  GRPRGPLWRSRKAIGKEALFVIQGLKRFKEDEEKFEKFMKSHVSRLLKLDMVAVLGELER 117

Query: 119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQ 178
           QEE  LAVKIF +IRKQDWY+PD YIYKDLIIALAR+ KM++AM++WESMR+E+LFPDSQ
Sbjct: 118 QEEVALAVKIFRLIRKQDWYKPDVYIYKDLIIALARSKKMDDAMKLWESMREENLFPDSQ 177

Query: 179 TYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEE 238
           TYTEVIRGFL+ GSP+DAMN+YEDM KSPDPP+ELPFRILLKGLLPHPLLR++VK+DFEE
Sbjct: 178 TYTEVIRGFLRYGSPSDAMNVYEDMKKSPDPPDELPFRILLKGLLPHPLLRNRVKQDFEE 237

Query: 239 LFPEKHAYDPPEEIFG 254
           LFP++H +DPPEEIF 
Sbjct: 238 LFPDQHVFDPPEEIFS 253

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232674|ref|NP_190271.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75266318|sp|Q9STF9.1|PP266_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At3g46870 gi|5541672|emb|CAB51178.1| putative protein [Arabidopsis thaliana] gi|26450732|dbj|BAC42475.1| unknown protein [Arabidopsis thaliana] gi|28950815|gb|AAO63331.1| At3g46870 [Arabidopsis thaliana] gi|332644692|gb|AEE78213.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 179/256 (69%), Positives = 217/256 (84%), Gaps = 2/256 (0%)

Query: 2   ATRLFSRSKIPILASIVLQNLTKNPS-KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGR 60
           A R+ SR K P  ASI  QN+T+NPS    SF   KPK+ +         + + ++HDGR
Sbjct: 3   AIRVCSR-KFPTFASIFFQNITRNPSIHRISFSNLKPKTLLHPIPPKPFTVFVSRFHDGR 61

Query: 61  PRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQE 120
           PRG LWRGKKLIGKEALFVILGLKR K+D+EKL KFIKTHV RLLK+D++AV+ ELERQE
Sbjct: 62  PRGPLWRGKKLIGKEALFVILGLKRLKEDDEKLDKFIKTHVFRLLKLDMLAVIGELERQE 121

Query: 121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY 180
           ET LA+K+F++I+KQ+WYQPD ++YKDLI++LA++ +M+EAM +WE M+KE+LFPDSQTY
Sbjct: 122 ETALAIKMFEVIQKQEWYQPDVFMYKDLIVSLAKSKRMDEAMALWEKMKKENLFPDSQTY 181

Query: 181 TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELF 240
           TEVIRGFL+DG PADAMN+YEDM+KSPDPPEELPFR+LLKGLLPHPLLR+KVKKDFEELF
Sbjct: 182 TEVIRGFLRDGCPADAMNVYEDMLKSPDPPEELPFRVLLKGLLPHPLLRNKVKKDFEELF 241

Query: 241 PEKHAYDPPEEIFGKL 256
           PEKHAYDPPEEIFG+ 
Sbjct: 242 PEKHAYDPPEEIFGRC 257

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224106373|ref|XP_002314145.1| predicted protein [Populus trichocarpa] gi|222850553|gb|EEE88100.1| predicted protein [Populus trichocarpa]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 190/260 (73%), Positives = 214/260 (82%), Gaps = 7/260 (2%)

Query: 1   MATRLFSRSKIPILASIV--LQNLTKNPSK-NFSFLAFKPKSPIVDFVAHEPILGLRQYH 57
           M TR  SRSKIP  +SI+  LQNLT   S  + + L     S I  F+      GLRQYH
Sbjct: 1   MLTRALSRSKIPNFSSIIVILQNLTTKQSIIDQTQLPLSKASNIQSFLVPA---GLRQYH 57

Query: 58  DGRPRGSLWRGKKLIGKEALFVILGLKRFK-DDEEKLQKFIKTHVLRLLKMDIVAVLIEL 116
           DGRPRG LWRGKKLIGKEALFVILGLKRFK DD+EKL +FIKTHV RLLK+D++AVL EL
Sbjct: 58  DGRPRGPLWRGKKLIGKEALFVILGLKRFKNDDDEKLDRFIKTHVFRLLKLDMIAVLSEL 117

Query: 117 ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD 176
           ERQEE  LAVKIF +I+KQDWY+PD Y+YKDLI+AL +TGKM EAM++WE MR EDLFPD
Sbjct: 118 ERQEEVSLAVKIFRVIQKQDWYKPDVYLYKDLIMALLKTGKMEEAMKLWEDMRNEDLFPD 177

Query: 177 SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDF 236
           SQ YTE IRG+L+DGSPADAMNIYEDM KSPDPPEELPFRILLKGLLPHPLLR++VK+D+
Sbjct: 178 SQMYTEAIRGYLRDGSPADAMNIYEDMKKSPDPPEELPFRILLKGLLPHPLLRNRVKQDY 237

Query: 237 EELFPEKHAYDPPEEIFGKL 256
           EELFPEKH YDPPEEIFG L
Sbjct: 238 EELFPEKHVYDPPEEIFGIL 257

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538964|ref|XP_003537970.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870-like [Glycine max]

 Score =  352 bits (904), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 176/257 (68%), Positives = 209/257 (81%), Gaps = 7/257 (2%)

Query: 1   MATRLFSRS-KIPILASIVLQNLTKN--PSKNFSFLAFKPKSPIVDFVAHEPILGLRQYH 57
           MA+R F ++ KI   AS++L   T++  P K+ S  +       V+F + +  L  RQYH
Sbjct: 1   MASRSFLKNWKILDFASLLLGEFTRSIKPIKDVSSTSLT----FVEFNSFKTALCFRQYH 56

Query: 58  DGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELE 117
           DGRPRG LW+GKKLIGKEALFVI G KRF DDE+KL KFIKTHVLRLLKMD++AVL ELE
Sbjct: 57  DGRPRGPLWKGKKLIGKEALFVISGFKRFNDDEDKLHKFIKTHVLRLLKMDMIAVLTELE 116

Query: 118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS 177
           RQE+  LA+ +F +++KQDWY+PDAY+YKDLIIALAR  KM+E +Q+WESMRKE+LFPDS
Sbjct: 117 RQEQVSLALMMFKVMQKQDWYKPDAYLYKDLIIALARAKKMDEVLQLWESMRKENLFPDS 176

Query: 178 QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFE 237
           QTYTEVIRGFL  GSPADAMNIYEDM  SPDPPEELPFRILLKGLLPHPLLR+KVK+DFE
Sbjct: 177 QTYTEVIRGFLNYGSPADAMNIYEDMKNSPDPPEELPFRILLKGLLPHPLLRNKVKQDFE 236

Query: 238 ELFPEKHAYDPPEEIFG 254
           E+FP+   YDPP+EIFG
Sbjct: 237 EIFPDSSIYDPPQEIFG 253

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357122492|ref|XP_003562949.1| PREDICTED: pentatricopeptide repeat-containing protein At3g46870-like [Brachypodium distachyon]

 Score =  320 bits (819), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 152/201 (75%), Positives = 176/201 (87%)

Query: 54  RQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVL 113
           R +HDGRPRG LWR KKLIGKEALF I GLKRFK DEEKL++F+K HV RLLK D +AVL
Sbjct: 44  RAFHDGRPRGPLWRSKKLIGKEALFAIQGLKRFKGDEEKLKEFVKRHVARLLKADKLAVL 103

Query: 114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDL 173
            ELERQEE  L+VK+F I++K+DWY+PD Y+YKDLIIALA+  KM EAM++W +MR E L
Sbjct: 104 GELERQEEVDLSVKMFRIVQKEDWYKPDVYMYKDLIIALAKCKKMEEAMEIWGNMRDEKL 163

Query: 174 FPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK 233
           FPDSQTY EVIRGFL+ GSP+DAMNIYEDM +SPDPPEELPFR+LLKGLLPHPLLR++VK
Sbjct: 164 FPDSQTYAEVIRGFLRYGSPSDAMNIYEDMKRSPDPPEELPFRVLLKGLLPHPLLRNRVK 223

Query: 234 KDFEELFPEKHAYDPPEEIFG 254
           +DFEELFPE+H YDPPEEIFG
Sbjct: 224 QDFEELFPERHIYDPPEEIFG 244

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326512702|dbj|BAK03258.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  316 bits (809), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 150/201 (74%), Positives = 178/201 (88%)

Query: 54  RQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVL 113
           R +HDGRPRG LWR KKLIGKEALF I GLKRFK DEEKL++FIK HV RLLK D +AVL
Sbjct: 49  RAFHDGRPRGPLWRSKKLIGKEALFAIQGLKRFKGDEEKLREFIKRHVARLLKADKLAVL 108

Query: 114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDL 173
            ELERQEE  L+VK+F II+K+DWY+PD Y+YKDLII+LA+  KM+EAM +W +M++E+L
Sbjct: 109 GELERQEEVDLSVKMFRIIQKEDWYKPDVYMYKDLIISLAKCKKMDEAMDIWGNMKEENL 168

Query: 174 FPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK 233
           FPDSQTY EVIRGFL+ GSP+DAMNIYEDM +SPDPPEELPFR+LLKGLLPHPLLR++VK
Sbjct: 169 FPDSQTYAEVIRGFLRYGSPSDAMNIYEDMKRSPDPPEELPFRVLLKGLLPHPLLRNRVK 228

Query: 234 KDFEELFPEKHAYDPPEEIFG 254
           +DFEELFPE+H YDPP++IFG
Sbjct: 229 QDFEELFPERHIYDPPDDIFG 249

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	256
TAIR|locus:2102832	257	AT3G46870 [Arabidopsis thalian	0.984	0.980	0.660	2.8e-89
TAIR|locus:2027149	196	AT1G62350 "AT1G62350" [Arabido	0.707	0.923	0.419	2.9e-39
TAIR|locus:2184727	712	VPS9B "AT5G09320" [Arabidopsis	0.625	0.224	0.298	3.9e-10
TAIR|locus:2081041	486	PPR2 "pentatricopeptide repeat	0.386	0.203	0.272	3e-07
TAIR|locus:2121529	727	EMB3131 "EMBRYO DEFECTIVE 3131	0.523	0.184	0.269	2.1e-06
TAIR|locus:2089154	222	EMB3123 "EMBRYO DEFECTIVE 3123	0.550	0.635	0.280	3.7e-06
TAIR|locus:2017754	718	AT1G22960 [Arabidopsis thalian	0.324	0.115	0.321	4.7e-06
TAIR|locus:2026172	485	NG1 "novel gene 1" [Arabidopsi	0.328	0.173	0.337	6e-06
TAIR|locus:2093472	642	AT3G16010 [Arabidopsis thalian	0.390	0.155	0.297	7e-06
TAIR|locus:2012883	537	AT1G20300 [Arabidopsis thalian	0.421	0.201	0.272	1.2e-05

TAIR|locus:2102832 AT3G46870 [Arabidopsis thaliana (taxid:3702)]

 Score = 891 (318.7 bits), Expect = 2.8e-89, P = 2.8e-89
 Identities = 169/256 (66%), Positives = 210/256 (82%)

Query:     2 ATRLFSRSKIPILASIVLQNLTKNPS-KNFSFLAFKPKSPIVDFVAHEPI-LGLRQYHDG 59
             A R+ SR K P  ASI  QN+T+NPS    SF   KPK+ ++  +  +P  + + ++HDG
Sbjct:     3 AIRVCSR-KFPTFASIFFQNITRNPSIHRISFSNLKPKT-LLHPIPPKPFTVFVSRFHDG 60

Query:    60 RPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQ 119
             RPRG LWRGKKLIGKEALFVILGLKR K+D+EKL KFIKTHV RLLK+D++AV+ ELERQ
Sbjct:    61 RPRGPLWRGKKLIGKEALFVILGLKRLKEDDEKLDKFIKTHVFRLLKLDMLAVIGELERQ 120

Query:   120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQT 179
             EET LA+K+F++I+KQ+WYQPD ++YKDLI++LA++ +M+EAM +WE M+KE+LFPDSQT
Sbjct:   121 EETALAIKMFEVIQKQEWYQPDVFMYKDLIVSLAKSKRMDEAMALWEKMKKENLFPDSQT 180

Query:   180 YTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIXXXXXXXXXXXRSKVKKDFEEL 239
             YTEVIRGFL+DG PADAMN+YEDM+KSPDPPEELPFR+           R+KVKKDFEEL
Sbjct:   181 YTEVIRGFLRDGCPADAMNVYEDMLKSPDPPEELPFRVLLKGLLPHPLLRNKVKKDFEEL 240

Query:   240 FPEKHAYDPPEEIFGK 255
             FPEKHAYDPPEEIFG+
Sbjct:   241 FPEKHAYDPPEEIFGR 256

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IDA

TAIR|locus:2027149 AT1G62350 "AT1G62350" [Arabidopsis thaliana (taxid:3702)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 76/181 (41%), Positives = 117/181 (64%)

Query:    72 IGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDI 131
             + KE L     LKR +    +L +FI +HV RLLK D+V+VL E +RQ +  L +K++++
Sbjct:     1 MSKEGLIAAKELKRLQTQSVRLDRFIGSHVSRLLKSDLVSVLAEFQRQNQVFLCMKLYEV 60

Query:   132 IRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG 191
             +R++ WY+PD + Y+D+++ LAR  K++E  +VWE ++KE++  D  T+ +++RGFL + 
Sbjct:    61 VRREIWYRPDMFFYRDMLMMLARNKKVDETKKVWEDLKKEEVLFDQHTFGDLVRGFLDNE 120

Query:   192 SPADAMNIYEDMIKSPDPPEELPFRIXXXXXXXXXXXRSKVKKDFEELFPEKHAYDPPEE 251
              P +AM +Y +M +SPD P  LPFR+           R KVK DF ELFP    YDPPE+
Sbjct:   121 LPLEAMRLYGEMRESPDRPLSLPFRVILKGLVPYPELREKVKDDFLELFPGMIVYDPPED 180

Query:   252 I 252
             I
Sbjct:   181 I 181

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2184727 VPS9B "AT5G09320" [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 3.9e-10, P = 3.9e-10
 Identities = 49/164 (29%), Positives = 78/164 (47%)

Query:    93 LQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL 152
             L + I +   RLLK D+VAVL EL RQ E  LA+K+F+ IRK+ WY+P   +Y D+I  +
Sbjct:   541 LDRVIISKFRRLLKFDMVAVLRELLRQNECSLALKVFEEIRKEYWYKPQVRMYTDMITVM 600

Query:   153 ARTGKMNEAMQVWESMRKED-LFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE 211
             A    M E   ++ +M+ E  L  + + +  ++   L        M+ Y  M      P+
Sbjct:   601 ADNSLMEEVNYLYSAMKSEKGLMAEIEWFNTLLTILLNHKLFDLVMDCYAFMQSIGYEPD 660

Query:   212 ELPFRIXXXXXXXXXXX--RSKVKKDFEELFPEKHAY-DPPEEI 252
                FR+              + V++D  E + E   + +  EEI
Sbjct:   661 RASFRVLVLGLESNGEMGLSAIVRQDAHEYYGESLEFIEEDEEI 704

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0006810 "transport" evidence=ISS

TAIR|locus:2081041 PPR2 "pentatricopeptide repeat 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 3.0e-07, P = 3.0e-07
 Identities = 27/99 (27%), Positives = 57/99 (57%)

Query:   109 IVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESM 168
             +   L +L  +++ + A+++FD++R+Q +YQP    Y  L++ L ++G+ N A ++++ M
Sbjct:    91 VTETLSDLIAKKQWLQALEVFDMLREQTFYQPKEGTYMKLLVLLGKSGQPNRAQKLFDEM 150

Query:   169 RKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP 207
              +E L P  + YT ++  + +     DA +I + M   P
Sbjct:   151 LEEGLEPTVELYTALLAAYTRSNLIDDAFSILDKMKSFP 189

GO:0005739 "mitochondrion" evidence=ISM

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

GO:0048868 "pollen tube development" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

GO:0009553 "embryo sac development" evidence=IMP

GO:0009555 "pollen development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0019843 "rRNA binding" evidence=IDA

TAIR|locus:2121529 EMB3131 "EMBRYO DEFECTIVE 3131" [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 38/141 (26%), Positives = 74/141 (52%)

Query:    71 LIGKEALFVIL--GLKRFKDDEEKLQKFIKTHVLRLLKMDIVA--VLIELERQEETILA- 125
             L+ +   F+IL  GL +    EE L+  ++     L K D+ A   +I+    E  + A 
Sbjct:   259 LVEESTTFMILVKGLCKAGRIEEMLE-ILQRMRENLCKPDVFAYTAMIKTLVSEGNLDAS 317

Query:   126 VKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIR 185
             ++++D +R+ D  +PD   Y  L++ L + G++    +++  M+ + +  D + Y  +I 
Sbjct:   318 LRVWDEMRR-DEIKPDVMAYGTLVVGLCKDGRVERGYELFMEMKGKQILIDREIYRVLIE 376

Query:   186 GFLKDGSPADAMNIYEDMIKS 206
             GF+ DG    A N++ED++ S
Sbjct:   377 GFVADGKVRSACNLWEDLVDS 397

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2089154 EMB3123 "EMBRYO DEFECTIVE 3123" [Arabidopsis thaliana (taxid:3702)]

 Score = 126 (49.4 bits), Expect = 3.7e-06, P = 3.7e-06
 Identities = 41/146 (28%), Positives = 72/146 (49%)

Query:    62 RGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEE 121
             RG L +G+ ++  EA+  I  LKR       L   ++  + RL+K D+++VL EL RQ+ 
Sbjct:    39 RGPLLKGR-ILSTEAIQSIQSLKRAHRTGVSLSLTLRP-LRRLIKSDLISVLRELLRQDY 96

Query:   122 TILAVKIFDIIRKQDWYQP-DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY 180
               LAV +   +R +  Y P D  +Y D++ AL R  + +E  ++   +   D   D +  
Sbjct:    97 CTLAVHVLSTLRTE--YPPLDLVLYADIVNALTRNKEFDEIDRLIGEIDGIDQRSDDKAL 154

Query:   181 TEVIRGFLKDGSPADAMNIYEDMIKS 206
              ++IR  +        + +Y  M +S
Sbjct:   155 AKLIRAVVGAERRESVVRVYTLMRES 180

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0000373 "Group II intron splicing" evidence=IMP

GO:0003723 "RNA binding" evidence=IDA

GO:0009658 "chloroplast organization" evidence=IMP

TAIR|locus:2017754 AT1G22960 [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 4.7e-06, P = 4.7e-06
 Identities = 27/84 (32%), Positives = 49/84 (58%)

Query:   128 IFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGF 187
             +FD +R  D + P    Y  LI  L  +G +  A ++ E M  + +FPD  TYT +++GF
Sbjct:   396 LFDDLRAGDIH-PSIVTYNTLIDGLCESGNLEGAQRLKEEMTTQLIFPDVITYTTLVKGF 454

Query:   188 LKDGSPADAMNIYEDMIKSPDPPE 211
             +K+G+ + A  +Y++M++    P+
Sbjct:   455 VKNGNLSMATEVYDEMLRKGIKPD 478

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2026172 NG1 "novel gene 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 6.0e-06, P = 6.0e-06
 Identities = 29/86 (33%), Positives = 51/86 (59%)

Query:   125 AVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVI 184
             AV++FD + + D  + DA  Y  L+  L  +G+ ++A ++   M   D+ P+  T+T VI
Sbjct:   193 AVELFDRMER-DGVRADAVTYNSLVAGLCCSGRWSDAARLMRDMVMRDIVPNVITFTAVI 251

Query:   185 RGFLKDGSPADAMNIYEDMIKS-PDP 209
               F+K+G  ++AM +YE+M +   DP
Sbjct:   252 DVFVKEGKFSEAMKLYEEMTRRCVDP 277

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009845 "seed germination" evidence=IMP

TAIR|locus:2093472 AT3G16010 [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 7.0e-06, P = 7.0e-06
 Identities = 30/101 (29%), Positives = 54/101 (53%)

Query:   111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK 170
             A++   E+      A+++FD + K +  QP   IY  L+    + GK+ +A+ ++E M++
Sbjct:   238 ALISSYEKLGRNDSAIRLFDEM-KDNCMQPTEKIYTTLLGIYFKVGKVEKALDLFEEMKR 296

Query:   171 EDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE 211
                 P   TYTE+I+G  K G   +A   Y+DM++    P+
Sbjct:   297 AGCSPTVYTYTELIKGLGKAGRVDEAYGFYKDMLRDGLTPD 337

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2012883 AT1G20300 [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 1.2e-05, P = 1.2e-05
 Identities = 30/110 (27%), Positives = 57/110 (51%)

Query:   106 KMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVW 165
             K+    V+  L R+     A   FD ++  D ++PD  +Y +L+    R G+++EA +V+
Sbjct:   221 KIAFSIVISNLSRKRRASEAQSFFDSLK--DRFEPDVIVYTNLVRGWCRAGEISEAEKVF 278

Query:   166 ESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPF 215
             + M+   + P+  TY+ VI    + G  + A +++ DM+ S   P  + F
Sbjct:   279 KEMKLAGIEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITF 328

GO:0005739 "mitochondrion" evidence=ISM;IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9STF9	PP266_ARATH	No assigned EC number	0.6992	0.9921	0.9883	yes	no

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	256
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-09
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-04
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	3e-04

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

 Score = 52.0 bits (126), Expect = 2e-09
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK 189
           PD   Y  LI    + GK+ EA++++  M+K  + P+  TY+ +I G  K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 44.7 bits (107), Expect = 8e-07
 Identities = 16/48 (33%), Positives = 25/48 (52%)

Query: 175 PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL 222
           PD  TY  +I G+ K G   +A+ ++ +M K    P    + IL+ GL
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 37.4 bits (88), Expect = 2e-04
 Identities = 10/35 (28%), Positives = 21/35 (60%)

Query: 143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS 177
             Y  LI  L + G++ EA+++++ M++  + PD 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. 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. Length = 35

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 41.4 bits (97), Expect = 3e-04
 Identities = 21/80 (26%), Positives = 41/80 (51%)

Query: 140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNI 199
           PD      L+ A A  G+++ A +V++ + + ++    + YT  +    + G    A++I
Sbjct: 577 PDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSI 636

Query: 200 YEDMIKSPDPPEELPFRILL 219
           Y+DM K    P+E+ F  L+
Sbjct: 637 YDDMKKKGVKPDEVFFSALV 656

Length = 1060

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	256
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PF13041	50	PPR_2: PPR repeat family	99.71
PF13041	50	PPR_2: PPR repeat family	99.7
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.57
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.53
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.35
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.34
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.33
PF12854	34	PPR_1: PPR repeat	99.32
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.28
PF12854	34	PPR_1: PPR repeat	99.23
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.98
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.9
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.89
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.86
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.86
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.81
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.79
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.74
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.71
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.67
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.66
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.66
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.64
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.64
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.57
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.55
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.55
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.42
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.36
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.27
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.25
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.24
KOG2003	840	consensus TPR repeat-containing protein [General f	98.21
PRK12370	553	invasion protein regulator; Provisional	98.21
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.18
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.16
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.12
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.12
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.1
PRK12370	553	invasion protein regulator; Provisional	98.09
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.08
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.06
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.06
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.06
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.05
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.99
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	97.94
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.93
PRK11189	296	lipoprotein NlpI; Provisional	97.93
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.91
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.88
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.87
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.85
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.84
PRK14574	822	hmsH outer membrane protein; Provisional	97.82
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.81
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.8
PRK14574	822	hmsH outer membrane protein; Provisional	97.79
PRK15359	144	type III secretion system chaperone protein SscB;	97.77
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.77
KOG1126	638	consensus DNA-binding cell division cycle control	97.76
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.74
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.71
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.65
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.64
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.62
PRK11189	296	lipoprotein NlpI; Provisional	97.6
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.55
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.52
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.5
KOG2003	840	consensus TPR repeat-containing protein [General f	97.5
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.49
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.49
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.48
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.46
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.46
PRK15359	144	type III secretion system chaperone protein SscB;	97.4
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.37
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.36
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.34
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.33
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.3
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.27
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.27
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.24
KOG1129	478	consensus TPR repeat-containing protein [General f	97.13
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.13
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.13
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.08
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.07
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.04
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.0
KOG2076	895	consensus RNA polymerase III transcription factor	96.99
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	96.99
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	96.98
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.98
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	96.97
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	96.95
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.94
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	96.9
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.9
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.87
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.87
KOG1126	638	consensus DNA-binding cell division cycle control	96.82
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.78
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.78
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.77
PF12688	120	TPR_5: Tetratrico peptide repeat	96.75
KOG3941	406	consensus Intermediate in Toll signal transduction	96.67
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.66
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.64
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.64
KOG2076	895	consensus RNA polymerase III transcription factor	96.62
PF12688	120	TPR_5: Tetratrico peptide repeat	96.58
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.58
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.58
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.57
KOG1129	478	consensus TPR repeat-containing protein [General f	96.56
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.51
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.49
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.44
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	96.42
KOG3941	406	consensus Intermediate in Toll signal transduction	96.39
KOG1125	579	consensus TPR repeat-containing protein [General f	96.34
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.31
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.3
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.18
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.13
PF13371	73	TPR_9: Tetratricopeptide repeat	96.1
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.08
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	95.99
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.89
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.85
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	95.82
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.79
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	95.76
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.69
PRK14720	906	transcript cleavage factor/unknown domain fusion p	95.58
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	95.5
KOG1915	677	consensus Cell cycle control protein (crooked neck	95.48
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.31
KOG0547	606	consensus Translocase of outer mitochondrial membr	95.28
KOG0553	304	consensus TPR repeat-containing protein [General f	95.25
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	95.02
PRK10803	263	tol-pal system protein YbgF; Provisional	95.0
KOG4340	459	consensus Uncharacterized conserved protein [Funct	94.97
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.97
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	94.96
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	94.83
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.76
KOG1128	777	consensus Uncharacterized conserved protein, conta	94.65
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.55
KOG3616	1636	consensus Selective LIM binding factor [Transcript	94.53
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	94.47
PF13371	73	TPR_9: Tetratricopeptide repeat	94.43
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	94.4
KOG2796	366	consensus Uncharacterized conserved protein [Funct	94.4
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	94.37
KOG2047	835	consensus mRNA splicing factor [RNA processing and	94.24
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	94.2
KOG0495	913	consensus HAT repeat protein [RNA processing and m	94.06
PRK14720	906	transcript cleavage factor/unknown domain fusion p	94.06
PRK10803	263	tol-pal system protein YbgF; Provisional	93.9
KOG1128	777	consensus Uncharacterized conserved protein, conta	93.81
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	93.69
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.56
KOG1125	579	consensus TPR repeat-containing protein [General f	93.51
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	93.48
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.43
KOG3060	289	consensus Uncharacterized conserved protein [Funct	93.27
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.22
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	93.14
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.11
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.07
KOG0553	304	consensus TPR repeat-containing protein [General f	93.04
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	92.89
KOG3785	557	consensus Uncharacterized conserved protein [Funct	92.76
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	92.75
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	92.65
smart00299	140	CLH Clathrin heavy chain repeat homology.	92.53
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	92.43
PF13762	145	MNE1: Mitochondrial splicing apparatus component	92.3
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	92.06
KOG2376	652	consensus Signal recognition particle, subunit Srp	91.89
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	91.77
PRK15331	165	chaperone protein SicA; Provisional	91.75
KOG4555	175	consensus TPR repeat-containing protein [Function	91.73
PF13512	142	TPR_18: Tetratricopeptide repeat	91.46
KOG3060	289	consensus Uncharacterized conserved protein [Funct	91.34
KOG1915	677	consensus Cell cycle control protein (crooked neck	91.24
COG4700	251	Uncharacterized protein conserved in bacteria cont	91.15
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	91.08
KOG4340	459	consensus Uncharacterized conserved protein [Funct	91.05
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	90.8
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	90.22
PF13762	145	MNE1: Mitochondrial splicing apparatus component	90.22
KOG4570	418	consensus Uncharacterized conserved protein [Funct	89.77
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	89.73
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	89.63
PRK04841	903	transcriptional regulator MalT; Provisional	89.58
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	89.41
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	89.29
PF09477	116	Type_III_YscG: Bacterial type II secretion system	89.03
PLN02789	320	farnesyltranstransferase	88.9
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	88.8
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	88.67
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.31
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	88.2
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	87.76
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	87.63
PF13512	142	TPR_18: Tetratricopeptide repeat	87.62
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	87.5
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	87.42
PF13428	44	TPR_14: Tetratricopeptide repeat	87.33
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	87.32
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	86.72
PF13428	44	TPR_14: Tetratricopeptide repeat	86.56
COG4455	273	ImpE Protein of avirulence locus involved in tempe	86.42
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	86.36
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	86.35
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	86.23
PRK04841	903	transcriptional regulator MalT; Provisional	86.21
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.06
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	85.82
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	85.82
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	85.45
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	85.37
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	85.1
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	84.84
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	84.61
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	84.45
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	84.22
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	83.88
KOG0495	913	consensus HAT repeat protein [RNA processing and m	83.82
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	83.75
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	82.97
PRK11906	458	transcriptional regulator; Provisional	82.96
PLN02789	320	farnesyltranstransferase	82.72
COG3118	304	Thioredoxin domain-containing protein [Posttransla	81.94
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	81.89
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	81.86
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	81.77
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	81.21
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	80.95
KOG2376	652	consensus Signal recognition particle, subunit Srp	80.83
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	80.53
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	80.5

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.5e-41  Score=313.93  Aligned_cols=245  Identities=11%  Similarity=0.086  Sum_probs=131.4

Q ss_pred             cccccccCCchHHHHHHHHHhcCCC------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccc---
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNPS------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIG---   73 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~~------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~---   73 (256)
                      |++|++.|+.+.|.++|++|.+.|+      |+++|.+|++.++++.+     +++|.+|...+..|+..+++.++.   
T Consensus       479 I~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeA-----l~lf~~M~~~Gv~PD~vTYnsLI~a~~  553 (1060)
T PLN03218        479 ISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKA-----FGAYGIMRSKNVKPDRVVFNALISACG  553 (1060)
T ss_pred             HHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHH-----HHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            4555666666666666666655443      56666666666655555     566666655555554443333321   


Q ss_pred             --------------------------hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHH
Q 025225           74 --------------------------KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETIL  124 (256)
Q Consensus        74 --------------------------~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~  124 (256)
                                                ..+..+|.+|++.|++++|. .+++.|.+.|+.|+..   ++|.+|++.|++++
T Consensus       554 k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~-elf~~M~e~gi~p~~~tynsLI~ay~k~G~~de  632 (1060)
T PLN03218        554 QSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAK-EVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDF  632 (1060)
T ss_pred             HCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHH-HHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHH
Confidence                                      12334455555555555554 3334555555554443   35555555555555


Q ss_pred             HHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          125 AVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       125 a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      |.++|++|.+.| +.||..||+++|.+|++.|++++|.++|++|.+.|+.||..+||+||.+|++.|++++|.++|++|.
T Consensus       633 Al~lf~eM~~~G-v~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~  711 (1060)
T PLN03218        633 ALSIYDDMKKKG-VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIK  711 (1060)
T ss_pred             HHHHHHHHHHcC-CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            555555555555 5555555555555555555555555555555555555555555555555555555555555555555


Q ss_pred             hCCCCCChhHHHHHHHHhcCCCChHHHHH----hhhhhcCCCcccccchhHhhc
Q 025225          205 KSPDPPEELPFRILLKGLLPHPLLRSKVK----KDFEELFPEKHAYDPPEEIFG  254 (256)
Q Consensus       205 ~~g~~p~~~t~~~li~~~~~~g~~~~a~~----~~~~~~~p~~~~~~~li~~y~  254 (256)
                      +.|+.||..|||+||.+|++.|++++|.+    |...|+.||..||+++|++|+
T Consensus       712 ~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~  765 (1060)
T PLN03218        712 SIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASE  765 (1060)
T ss_pred             HcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            55555555555555555555555555555    444555555555555555554

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=9.1e-41  Score=310.21  Aligned_cols=238  Identities=15%  Similarity=0.111  Sum_probs=144.6

Q ss_pred             ccccccccCCchHHHHHHHHHhcCCC------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchh
Q 025225            2 ATRLFSRSKIPILASIVLQNLTKNPS------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKE   75 (256)
Q Consensus         2 ~i~~~~~~~~~~~A~~l~~~m~~~~~------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~   75 (256)
                      .|++|++.|+.+.|.++|+.|.+.|+      |+++|.+|++.++++.+     .++|++|...+..|+..+++.+    
T Consensus       443 LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A-----~~vf~eM~~~Gv~PdvvTynaL----  513 (1060)
T PLN03218        443 LMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAM-----FEVFHEMVNAGVEANVHTFGAL----  513 (1060)
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHH-----HHHHHHHHHcCCCCCHHHHHHH----
Confidence            46788999999999999999998876      99999999999999888     9999999988888866665554    


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHh--cCCCCCCHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRK--QDWYQPDAYIYKDLII  150 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~--~~~~~p~~~~y~~li~  150 (256)
                          |.+|++.|+.++|+ .+++.|...|+.||..   ++|++|++.|++++|.++|++|.+  .| +.||.+||+++|.
T Consensus       514 ----I~gy~k~G~~eeAl-~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~g-i~PD~vTynaLI~  587 (1060)
T PLN03218        514 ----IDGCARAGQVAKAF-GAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHP-IDPDHITVGALMK  587 (1060)
T ss_pred             ----HHHHHHCcCHHHHH-HHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCC-CCCcHHHHHHHHH
Confidence                55555555555554 3334555555555543   355555555555555555555543  23 4555555555555


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          151 ALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       151 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      +|++.|++++|.++|++|.+.|+.|+..+||++|.+|++.|++++|.++|++|.+.|+.||..||+++|++|++.|++++
T Consensus       588 ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~ee  667 (1060)
T PLN03218        588 ACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDK  667 (1060)
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHH
Confidence            55555555555555555555555555555555555555555555555555555555555555555555555555555554


Q ss_pred             HHH----hhhhhcCCCcccccchhHhhc
Q 025225          231 KVK----KDFEELFPEKHAYDPPEEIFG  254 (256)
Q Consensus       231 a~~----~~~~~~~p~~~~~~~li~~y~  254 (256)
                      |.+    |...|+.||..+|++||++|+
T Consensus       668 A~~l~~eM~k~G~~pd~~tynsLI~ay~  695 (1060)
T PLN03218        668 AFEILQDARKQGIKLGTVSYSSLMGACS  695 (1060)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            444    344444445445555554444

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

Probab=100.00  E-value=4.1e-40  Score=300.65  Aligned_cols=243  Identities=14%  Similarity=0.135  Sum_probs=216.6

Q ss_pred             ccccccccCCchHHHHHHHHHhcCCC--ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccccc---------
Q 025225            2 ATRLFSRSKIPILASIVLQNLTKNPS--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKK---------   70 (256)
Q Consensus         2 ~i~~~~~~~~~~~A~~l~~~m~~~~~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~---------   70 (256)
                      .|++|++.|+.+.|.++|++|.+.+.  ||+++++|++.++++.+     +.+|++|...+..|+..++..         
T Consensus       164 Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A-----~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~  238 (697)
T PLN03081        164 VLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREA-----FALFREMWEDGSDAEPRTFVVMLRASAGLG  238 (697)
T ss_pred             HHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHH-----HHHHHHHHHhCCCCChhhHHHHHHHHhcCC
Confidence            36788999999999999999988776  99999999999988888     999999987776665443322         


Q ss_pred             --------------------------cc-----------------------chhHHHHHHHhhcCCCcHHHHHHHHHHHh
Q 025225           71 --------------------------LI-----------------------GKEALFVILGLKRFKDDEEKLQKFIKTHV  101 (256)
Q Consensus        71 --------------------------~~-----------------------~~~~~~~i~~~~~~~~~~~a~~~~~~~~~  101 (256)
                                                ++                       ...|..+|.+|++.|+.++|+ .++++|.
T Consensus       239 ~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~-~lf~~M~  317 (697)
T PLN03081        239 SARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEAL-CLYYEMR  317 (697)
T ss_pred             cHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHH-HHHHHHH
Confidence                                      11                       126788899999999999998 5668899


Q ss_pred             hccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHh
Q 025225          102 LRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQ  178 (256)
Q Consensus       102 ~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  178 (256)
                      +.|+.||..   ++|++|++.|++++|.++|++|.+.| +.||..+||+||++|+++|++++|.++|++|.+    ||+.
T Consensus       318 ~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g-~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~  392 (697)
T PLN03081        318 DSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTG-FPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLI  392 (697)
T ss_pred             HcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhC-CCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCee
Confidence            999999887   49999999999999999999999999 999999999999999999999999999999986    8999


Q ss_pred             hHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH----hh-hhhcCCCcccccchhHhh
Q 025225          179 TYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK----KD-FEELFPEKHAYDPPEEIF  253 (256)
Q Consensus       179 t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~----~~-~~~~~p~~~~~~~li~~y  253 (256)
                      |||+||.+|++.|+.++|.++|++|.+.|++||..||+++|.+|++.|.+++|.+    |. ..++.|+..+|+++|++|
T Consensus       393 t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l  472 (697)
T PLN03081        393 SWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELL  472 (697)
T ss_pred             eHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHH
Confidence            9999999999999999999999999999999999999999999999999999988    43 368999999999999999


Q ss_pred             cc
Q 025225          254 GK  255 (256)
Q Consensus       254 ~~  255 (256)
                      ++
T Consensus       473 ~r  474 (697)
T PLN03081        473 GR  474 (697)
T ss_pred             Hh
Confidence            86

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

Probab=100.00  E-value=2.4e-38  Score=289.01  Aligned_cols=235  Identities=14%  Similarity=0.138  Sum_probs=213.8

Q ss_pred             ccccccccCCchHHHHHHHHHhcCCC--ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            2 ATRLFSRSKIPILASIVLQNLTKNPS--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         2 ~i~~~~~~~~~~~A~~l~~~m~~~~~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .|.+|+++|+.++|.++|++|.+.+.  ||+++.+|++.++.+.+     +++|++|...+..|+..        ++..+
T Consensus       265 Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA-----~~lf~~M~~~g~~pd~~--------t~~~l  331 (697)
T PLN03081        265 LIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEA-----LCLYYEMRDSGVSIDQF--------TFSIM  331 (697)
T ss_pred             HHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHH-----HHHHHHHHHcCCCCCHH--------HHHHH
Confidence            36789999999999999999988876  99999999999999999     99999999988888444        55566


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      +.+|++.|..+++. .++..|.+.|+.||..   +||++|++.|++++|.++|++|.     .||+.+||+||.+|++.|
T Consensus       332 l~a~~~~g~~~~a~-~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~-----~~d~~t~n~lI~~y~~~G  405 (697)
T PLN03081        332 IRIFSRLALLEHAK-QAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-----RKNLISWNALIAGYGNHG  405 (697)
T ss_pred             HHHHHhccchHHHH-HHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC-----CCCeeeHHHHHHHHHHcC
Confidence            99999999999997 6778999999999876   69999999999999999999986     579999999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHh-CCCCCChhHHHHHHHHhcCCCChHHHHH-h
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIK-SPDPPEELPFRILLKGLLPHPLLRSKVK-K  234 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~-~g~~p~~~t~~~li~~~~~~g~~~~a~~-~  234 (256)
                      +.++|.++|++|.+.|+.||.+||+++|.+|++.|++++|.++|++|.+ .|+.|+..+|++||++|++.|++++|.+ .
T Consensus       406 ~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~  485 (697)
T PLN03081        406 RGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMI  485 (697)
T ss_pred             CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999986 5999999999999999999999999998 4


Q ss_pred             hhhhcCCCcccccchhHhhcc
Q 025225          235 DFEELFPEKHAYDPPEEIFGK  255 (256)
Q Consensus       235 ~~~~~~p~~~~~~~li~~y~~  255 (256)
                      ...++.|+..+|++|+++|..
T Consensus       486 ~~~~~~p~~~~~~~Ll~a~~~  506 (697)
T PLN03081        486 RRAPFKPTVNMWAALLTACRI  506 (697)
T ss_pred             HHCCCCCCHHHHHHHHHHHHH
Confidence            445678999999999988753

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.6e-37  Score=288.08  Aligned_cols=246  Identities=13%  Similarity=0.200  Sum_probs=202.1

Q ss_pred             cccccccCCchHHHHHHHHHhcCCC--ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccccccc--------
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNPS--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLI--------   72 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~--------   72 (256)
                      |.+|+++|+.+.|.++|++|.+.+.  ||+++++|++.+...++     +.+|.+|...+..|+..+++.++        
T Consensus       229 i~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eA-----l~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~  303 (857)
T PLN03077        229 ITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEG-----LELFFTMRELSVDPDLMTITSVISACELLGD  303 (857)
T ss_pred             HHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHH-----HHHHHHHHHcCCCCChhHHHHHHHHHHhcCC
Confidence            5667777777777777777776655  77777777777777777     77777777766666655544433        


Q ss_pred             --------------------------------------------------chhHHHHHHHhhcCCCcHHHHHHHHHHHhh
Q 025225           73 --------------------------------------------------GKEALFVILGLKRFKDDEEKLQKFIKTHVL  102 (256)
Q Consensus        73 --------------------------------------------------~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~  102 (256)
                                                                        ...|..+|.+|++.|+.++|+ .++++|.+
T Consensus       304 ~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~-~lf~~M~~  382 (857)
T PLN03077        304 ERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKAL-ETYALMEQ  382 (857)
T ss_pred             hHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHH-HHHHHHHH
Confidence                                                              126788899999999999997 56688999


Q ss_pred             ccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-------
Q 025225          103 RLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKED-------  172 (256)
Q Consensus       103 ~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-------  172 (256)
                      .|+.||..   ++|.+|++.|++++|.++|+.|.+.| +.|+..+||+||.+|+++|++++|.++|++|.+.+       
T Consensus       383 ~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g-~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~m  461 (857)
T PLN03077        383 DNVSPDEITIASVLSACACLGDLDVGVKLHELAERKG-LISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSI  461 (857)
T ss_pred             hCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHH
Confidence            99999876   58999999999999999999999998 88999999999999999998888888888875532       


Q ss_pred             -----------------------C--------------------------------------------------------
Q 025225          173 -----------------------L--------------------------------------------------------  173 (256)
Q Consensus       173 -----------------------~--------------------------------------------------------  173 (256)
                                             +                                                        
T Consensus       462 i~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~  541 (857)
T PLN03077        462 IAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMN  541 (857)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHH
Confidence                                   1                                                        


Q ss_pred             ---------CCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH----hh-hhhc
Q 025225          174 ---------FPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK----KD-FEEL  239 (256)
Q Consensus       174 ---------~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~----~~-~~~~  239 (256)
                               .||+++||+||.+|++.|+.++|.++|++|.+.|+.||..||+++|.+|++.|++++|.+    |. ..++
T Consensus       542 ~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi  621 (857)
T PLN03077        542 YAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSI  621 (857)
T ss_pred             HHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCC
Confidence                     456777888889999999999999999999999999999999999999999999999887    55 5788


Q ss_pred             CCCcccccchhHhhcc
Q 025225          240 FPEKHAYDPPEEIFGK  255 (256)
Q Consensus       240 ~p~~~~~~~li~~y~~  255 (256)
                      .|+..+|++||++|++
T Consensus       622 ~P~~~~y~~lv~~l~r  637 (857)
T PLN03077        622 TPNLKHYACVVDLLGR  637 (857)
T ss_pred             CCchHHHHHHHHHHHh
Confidence            9999999999999886

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=6.7e-37  Score=285.32  Aligned_cols=242  Identities=18%  Similarity=0.171  Sum_probs=202.3

Q ss_pred             cccccccCCchHHHHHHHHHhcCCC--ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccc---------
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNPS--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKL---------   71 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~---------   71 (256)
                      |+.|++.|+.+.|.++|++|.+.+.  ||+++++|++.+.++.+     +.+|++|...+..|+..+++.+         
T Consensus       128 i~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~~~~~~g~~~~A-----~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~  202 (857)
T PLN03077        128 LSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEA-----LCLYHRMLWAGVRPDVYTFPCVLRTCGGIPD  202 (857)
T ss_pred             HHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHHHHHhCCCHHHH-----HHHHHHHHHcCCCCChhHHHHHHHHhCCccc
Confidence            5567777777777777777776665  77777777777777777     7777777766666665544322         


Q ss_pred             --------------------------c-----------------------chhHHHHHHHhhcCCCcHHHHHHHHHHHhh
Q 025225           72 --------------------------I-----------------------GKEALFVILGLKRFKDDEEKLQKFIKTHVL  102 (256)
Q Consensus        72 --------------------------~-----------------------~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~  102 (256)
                                                +                       ...|..+|.+|++.|+.++|+ .++++|..
T Consensus       203 ~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl-~lf~~M~~  281 (857)
T PLN03077        203 LARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGL-ELFFTMRE  281 (857)
T ss_pred             hhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHH-HHHHHHHH
Confidence                                      1                       126777888888888888887 56678888


Q ss_pred             ccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhh
Q 025225          103 RLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQT  179 (256)
Q Consensus       103 ~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  179 (256)
                      .|+.||..   ++|.+|++.|+++.|.+++..|.+.| +.||+.+||+||.+|+++|++++|.++|++|.+    ||.++
T Consensus       282 ~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g-~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~~s  356 (857)
T PLN03077        282 LSVDPDLMTITSVISACELLGDERLGREMHGYVVKTG-FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVS  356 (857)
T ss_pred             cCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhC-CccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----CCeee
Confidence            99999877   48999999999999999999999999 899999999999999999999999999999975    89999


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH----hhhhhcCCCcccccchhHhhcc
Q 025225          180 YTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK----KDFEELFPEKHAYDPPEEIFGK  255 (256)
Q Consensus       180 ~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~----~~~~~~~p~~~~~~~li~~y~~  255 (256)
                      ||++|.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++|.+    +...|+.|+..+||+||++|++
T Consensus       357 ~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k  436 (857)
T PLN03077        357 WTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSK  436 (857)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999998888    6778888999999999998875

>PF13041 PPR_2: PPR repeat family

Probab=99.71  E-value=3.1e-17  Score=98.27  Aligned_cols=50  Identities=32%  Similarity=0.653  Sum_probs=28.0

Q ss_pred             CCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC
Q 025225          175 PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP  224 (256)
Q Consensus       175 p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~  224 (256)
                      ||+++||++|++|++.|++++|.++|++|.+.|++||..||++||++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            45555555555555555555555555555555555555555555555543

>PF13041 PPR_2: PPR repeat family

Probab=99.70  E-value=4.8e-17  Score=97.43  Aligned_cols=50  Identities=38%  Similarity=0.711  Sum_probs=49.1

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK  189 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  189 (256)
                      ||+++||++|.+|++.|++++|.++|++|++.|+.||..||++||++|||
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            89999999999999999999999999999999999999999999999985

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.57  E-value=1.1e-13  Score=118.69  Aligned_cols=135  Identities=10%  Similarity=-0.001  Sum_probs=72.3

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCC
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGS  192 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~  192 (256)
                      ...+.+.|++++|...|+++.+..  ..+...+..+...|.+.|++++|.++|+++.+.+-.....+++.+..+|++.|+
T Consensus       187 a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~  264 (389)
T PRK11788        187 AQQALARGDLDAARALLKKALAAD--PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGD  264 (389)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhHC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCC
Confidence            334445566666666666655443  233445555556666666666666666665543211113445566666666666


Q ss_pred             hhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhh--hhhcCCCcccccchhH
Q 025225          193 PADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKD--FEELFPEKHAYDPPEE  251 (256)
Q Consensus       193 ~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~--~~~~~p~~~~~~~li~  251 (256)
                      +++|.+.++++.+.  .|+...+..+...+.+.|++++|....  .-...|+..+++.+++
T Consensus       265 ~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~  323 (389)
T PRK11788        265 EAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLD  323 (389)
T ss_pred             HHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHH
Confidence            66666666665554  344445555666666666666665521  2223455555554444

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.53  E-value=3.2e-13  Score=115.73  Aligned_cols=223  Identities=11%  Similarity=0.032  Sum_probs=166.7

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .|.+.|+.+.|.++|+++.+...     ++.+...+...++...+     +..++.+....+.+...    .....+..+
T Consensus       116 ~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~~~~~~~~~~~~----~~~~~~~~l  186 (389)
T PRK11788        116 DYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKA-----IDVAERLEKLGGDSLRV----EIAHFYCEL  186 (389)
T ss_pred             HHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHH-----HHHHHHHHHhcCCcchH----HHHHHHHHH
Confidence            45677888888888888865322     66677777777777777     88887776544322110    011123344


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ...+.+.++.++|.. .++.+.+..  |+..    .+...+.+.|++++|.+.|+++.+.+ ......+++.+..+|.+.
T Consensus       187 a~~~~~~~~~~~A~~-~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~l~~~~~~~  262 (389)
T PRK11788        187 AQQALARGDLDAARA-LLKKALAAD--PQCVRASILLGDLALAQGDYAAAIEALERVEEQD-PEYLSEVLPKLMECYQAL  262 (389)
T ss_pred             HHHHHhCCCHHHHHH-HHHHHHhHC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-hhhHHHHHHHHHHHHHHc
Confidence            556788999999985 445554432  3322    47788999999999999999999765 233356789999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC---CCChHHHH
Q 025225          156 GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP---HPLLRSKV  232 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~---~g~~~~a~  232 (256)
                      |++++|.+.++++.+.  .|+...+..+...+.+.|++++|..+++++.+.  .|+..+++.++..+..   .|+.++++
T Consensus       263 g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~  338 (389)
T PRK11788        263 GDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESL  338 (389)
T ss_pred             CCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHH
Confidence            9999999999999885  477778899999999999999999999998876  6999999999988774   55777776


Q ss_pred             H----hhhhhcCCCcc
Q 025225          233 K----KDFEELFPEKH  244 (256)
Q Consensus       233 ~----~~~~~~~p~~~  244 (256)
                      .    +...++.|++.
T Consensus       339 ~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        339 LLLRDLVGEQLKRKPR  354 (389)
T ss_pred             HHHHHHHHHHHhCCCC
Confidence            5    55567777654

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

Probab=99.35  E-value=5.4e-11  Score=111.46  Aligned_cols=117  Identities=14%  Similarity=0.092  Sum_probs=48.4

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +...+.+.|++++|..+|+.+.+..  +.+..++..+...+...|++++|.++++.+.+.+ .++...+..+...|.+.|
T Consensus       641 l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g  717 (899)
T TIGR02917       641 LADAYAVMKNYAKAITSLKRALELK--PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQK  717 (899)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCC
Confidence            3344444444444444444444332  2334444444444444444444444444444332 123333444444444444


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++++|.+.|+++.+.+  |+..++..+...+.+.|++++|.+
T Consensus       718 ~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~  757 (899)
T TIGR02917       718 DYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVK  757 (899)
T ss_pred             CHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHH
Confidence            4444444444444332  222333334444444444444433

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.

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.34  E-value=2.5e-11  Score=100.59  Aligned_cols=115  Identities=15%  Similarity=0.145  Sum_probs=103.6

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .||.++|+-..++.|.+++++-.... .+.+..+||.+|.+-.-..+    .++..+|....+.||..|||+++++.++.
T Consensus       212 ~mI~Gl~K~~~~ERA~~L~kE~~~~k-~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL~c~akf  286 (625)
T KOG4422|consen  212 IMIAGLCKFSSLERARELYKEHRAAK-GKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALLSCAAKF  286 (625)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHhh-heeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHHHHHHHh
Confidence            59999999999999999999988776 69999999999987665433    78999999999999999999999999999


Q ss_pred             CChhH----HHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          191 GSPAD----AMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       191 g~~~~----a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      |+++.    |.+++.+|++.|+.|+..+|..+|..+++.++-.+
T Consensus       287 g~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  287 GKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             cchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh
Confidence            98775    56889999999999999999999999999987644

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

Probab=99.33  E-value=7e-11  Score=110.71  Aligned_cols=207  Identities=17%  Similarity=0.122  Sum_probs=132.6

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .|.+.|+++.|.++++.+.+...     |..+...+...++.+.+     +..|+.+....+..         ...+..+
T Consensus       576 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l  641 (899)
T TIGR02917       576 YYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKA-----VSSFKKLLALQPDS---------ALALLLL  641 (899)
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHhCCCC---------hHHHHHH
Confidence            35556677777777776654322     55555566666666666     67776665433211         1234445


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ...+.+.|+.++|+..+ +...+.  .|+..    .+...+...|++++|.++++.+.+.+  ..+...+..+...+.+.
T Consensus       642 ~~~~~~~~~~~~A~~~~-~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~  716 (899)
T TIGR02917       642 ADAYAVMKNYAKAITSL-KRALEL--KPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH--PKAALGFELEGDLYLRQ  716 (899)
T ss_pred             HHHHHHcCCHHHHHHHH-HHHHhc--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cCChHHHHHHHHHHHHC
Confidence            66677788888887444 344332  23211    46777777788888888888877775  56667777777777777


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          156 GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |++++|.+.|+++...+  |+..++..+...|.+.|+.++|.+.++++.+.. +.+...+..+...|...|++++|.+
T Consensus       717 g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~  791 (899)
T TIGR02917       717 KDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIK  791 (899)
T ss_pred             CCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHH
Confidence            88888877777776643  555666667777777777777777777766542 3355666666677777777777766

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.

>PF12854 PPR_1: PPR repeat

Probab=99.32  E-value=2.2e-12  Score=70.03  Aligned_cols=32  Identities=31%  Similarity=0.660  Sum_probs=20.1

Q ss_pred             CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          172 DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       172 g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      |+.||.+|||+||.+||+.|++++|.++|++|
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            55666666666666666666666666666665

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.28  E-value=8.5e-11  Score=97.46  Aligned_cols=169  Identities=10%  Similarity=0.062  Sum_probs=128.7

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHH--HcCCHH-HHHHHHHHHHhcC------------------C
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELE--RQEETI-LAVKIFDIIRKQD------------------W  137 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~--~~~~~~-~a~~~~~~m~~~~------------------~  137 (256)
                      -...+|.+++++ .++..|...|+..+-.   .|++.-+  .+.++- .-.+-|=.|.+.|                  .
T Consensus       124 kmIS~~EvKDs~-ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~  202 (625)
T KOG4422|consen  124 KMISSREVKDSC-ILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFET  202 (625)
T ss_pred             HHHhhcccchhH-HHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhh
Confidence            345678899987 7788898888755443   3333322  222211 1111122222222                  0


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHH
Q 025225          138 YQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRI  217 (256)
Q Consensus       138 ~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~  217 (256)
                      ...+..||.+||.++|+.-..+.|.+++++-.....+.+..+||.+|.+-.-.    ....+..+|.+..++||..|||+
T Consensus       203 ~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~----~~K~Lv~EMisqkm~Pnl~TfNa  278 (625)
T KOG4422|consen  203 LPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYS----VGKKLVAEMISQKMTPNLFTFNA  278 (625)
T ss_pred             cCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhh----ccHHHHHHHHHhhcCCchHhHHH
Confidence            34577899999999999999999999999999988899999999999875432    23889999999999999999999


Q ss_pred             HHHHhcCCCChHHHHH--------hhhhhcCCCcccccchhHhhcc
Q 025225          218 LLKGLLPHPLLRSKVK--------KDFEELFPEKHAYDPPEEIFGK  255 (256)
Q Consensus       218 li~~~~~~g~~~~a~~--------~~~~~~~p~~~~~~~li~~y~~  255 (256)
                      ++.+.++.|+++.|.+        |+.-|++|...+|.-+|..|.+
T Consensus       279 lL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~r  324 (625)
T KOG4422|consen  279 LLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKR  324 (625)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcc
Confidence            9999999999888776        8889999999999999987754

>PF12854 PPR_1: PPR repeat

Probab=99.23  E-value=1.6e-11  Score=66.64  Aligned_cols=33  Identities=27%  Similarity=0.675  Sum_probs=31.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225          136 DWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus       136 ~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      | +.||.+|||+||++||+.|++++|.++|++|+
T Consensus         2 G-~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 G-CEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             C-CCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            5 89999999999999999999999999999995

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

Probab=98.98  E-value=2.2e-09  Score=88.04  Aligned_cols=210  Identities=14%  Similarity=0.055  Sum_probs=76.0

Q ss_pred             cccccCCchHHHHHHHH-HhcC-CC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHH
Q 025225            5 LFSRSKIPILASIVLQN-LTKN-PS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEAL   77 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~-m~~~-~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~   77 (256)
                      .+-+.|+++.|+++++. .... +.     |..+-.-....++.+.+     +..++++...+... ...+..       
T Consensus        17 ~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A-----~~ay~~l~~~~~~~-~~~~~~-------   83 (280)
T PF13429_consen   17 LLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEA-----IEAYEKLLASDKAN-PQDYER-------   83 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccc-----cccccccccccccc-cccccc-------
Confidence            45678999999999954 4333 22     44433333444556666     77777776543221 111111       


Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                        +..+...+++++|+..+..... +.-.|... .++..+.+.++++++.++++...+......+...|..+-..+.+.|
T Consensus        84 --l~~l~~~~~~~~A~~~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G  160 (280)
T PF13429_consen   84 --LIQLLQDGDPEEALKLAEKAYE-RDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLG  160 (280)
T ss_dssp             -------------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCC
T ss_pred             --cccccccccccccccccccccc-cccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcC
Confidence              2222466777777644332222 22223322 4666677777777777777776654434566677777777777777


Q ss_pred             CHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +.++|.+.+++..+.  .|+ ....+.++..+...|+.+++.+++....+.. ..|+..+..+..+|...|+.++|+.
T Consensus       161 ~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~  235 (280)
T PF13429_consen  161 DPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALE  235 (280)
T ss_dssp             HHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHH
T ss_pred             CHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccc
Confidence            777777777777663  354 5666777777777777777777777666553 4455566777777777777777777

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.90  E-value=2.4e-09  Score=58.49  Aligned_cols=33  Identities=27%  Similarity=0.646  Sum_probs=21.7

Q ss_pred             hHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC
Q 025225          179 TYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE  211 (256)
Q Consensus       179 t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~  211 (256)
                      |||++|.+|++.|++++|.++|++|.+.|++||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            566666666666666666666666666666665

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

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

Probab=98.89  E-value=6.5e-08  Score=86.90  Aligned_cols=203  Identities=9%  Similarity=-0.010  Sum_probs=137.1

Q ss_pred             HHHHHHhcCCC------ccccccccCCCCCCCCcccCcccccccccccCC--CCCCccc--------------cccccch
Q 025225           17 IVLQNLTKNPS------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGR--PRGSLWR--------------GKKLIGK   74 (256)
Q Consensus        17 ~l~~~m~~~~~------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~--~~~~~~~--------------~~~~~~~   74 (256)
                      +++..++..|+      |..+|.-||..|+++.+     - +|.-|....  +...+++              .......
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaa-----t-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aD   84 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAA-----T-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLAD   84 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCccc-----c-chhhhhcccccccchhHHHHHhcccccccccCCCCCchh
Confidence            45666777766      88889888888888776     3 554443222  2211111              1112245


Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHh------------------------hccCCCcHHHHHHHHHHcCCHHHHHHHH-
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHV------------------------LRLLKMDIVAVLIELERQEETILAVKIF-  129 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~------------------------~~~~~~~~~~li~~~~~~~~~~~a~~~~-  129 (256)
                      .|..+..+|.++|+... ++..-+.+.                        ..+.-||..+.+.-....|.++.+.++. 
T Consensus        85 tyt~Ll~ayr~hGDli~-fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~  163 (1088)
T KOG4318|consen   85 TYTNLLKAYRIHGDLIL-FEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLA  163 (1088)
T ss_pred             HHHHHHHHHHhccchHH-HHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHh
Confidence            88999999999998765 333322221                        1223455544444444444444444443 


Q ss_pred             -----------------------------HHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhH
Q 025225          130 -----------------------------DIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY  180 (256)
Q Consensus       130 -----------------------------~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  180 (256)
                                                   +..++-. -.|++.+|..++..-.-+|+++.|..++.+|++.|+..+..-|
T Consensus       164 ~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~-e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyF  242 (1088)
T KOG4318|consen  164 KVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLV-EAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYF  242 (1088)
T ss_pred             hCCcccccchHHHHHHHhccCCchHHHHHHHHHHhh-cCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccc
Confidence                                         2222222 2589999999999999999999999999999999998888888


Q ss_pred             HHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          181 TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       181 ~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      -.||-+   .++..-+..+.+.|.+.|+.|++.|+...+-.+.++|....
T Consensus       243 wpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t~~  289 (1088)
T KOG4318|consen  243 WPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQTKY  289 (1088)
T ss_pred             hhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhhhh
Confidence            888877   78888889999999999999999999988888877665443

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.86  E-value=3.5e-07  Score=83.64  Aligned_cols=115  Identities=10%  Similarity=0.021  Sum_probs=50.8

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhH
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPAD  195 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~  195 (256)
                      +...|++++|...++.+.+.. ..++...+..+...+.+.|++++|...|++..+.. ..+...+..+-..|.+.|++++
T Consensus       187 l~~~g~~~eA~~~~~~~l~~~-~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~e  264 (656)
T PRK15174        187 FLNKSRLPEDHDLARALLPFF-ALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSRE  264 (656)
T ss_pred             HHHcCCHHHHHHHHHHHHhcC-CCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchh
Confidence            334444444444444443332 11222233333344444455555555555444321 1123344444445555555543


Q ss_pred             ----HHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          196 ----AMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       196 ----a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                          |...|++..+.. ..+...+..+...+.+.|++++|+.
T Consensus       265 A~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~  305 (656)
T PRK15174        265 AKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIP  305 (656)
T ss_pred             hHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence                455555444431 1133445555555555555555555

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.86  E-value=2.7e-07  Score=84.44  Aligned_cols=146  Identities=10%  Similarity=0.036  Sum_probs=103.9

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      .+.+.|+.++|... ++.+....-.++..   .+..++.+.|++++|...|++..+..  ..+...+..+-..|...|++
T Consensus       186 ~l~~~g~~~eA~~~-~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~--p~~~~~~~~Lg~~l~~~G~~  262 (656)
T PRK15174        186 SFLNKSRLPEDHDL-ARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG--LDGAALRRSLGLAYYQSGRS  262 (656)
T ss_pred             HHHHcCCHHHHHHH-HHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCc
Confidence            35667777777643 34443332111111   24567778888999999998888775  55677888888888888888


Q ss_pred             HH----HHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          159 NE----AMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       159 ~~----a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++    |...|++..+.  .| +...+..+-..+.+.|++++|...+++..+... -+...+..+...|.+.|++++|..
T Consensus       263 ~eA~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P-~~~~a~~~La~~l~~~G~~~eA~~  339 (656)
T PRK15174        263 REAKLQAAEHWRHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHP-DLPYVRAMYARALRQVGQYTAASD  339 (656)
T ss_pred             hhhHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHH
Confidence            85    78888887763  34 456788888888888899999988888776532 234456677788888888888887

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.81  E-value=6.5e-09  Score=56.69  Aligned_cols=35  Identities=29%  Similarity=0.596  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS  177 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  177 (256)
                      ++||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999984

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.79  E-value=8.8e-09  Score=55.90  Aligned_cols=33  Identities=27%  Similarity=0.628  Sum_probs=20.5

Q ss_pred             hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC
Q 025225          178 QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP  210 (256)
Q Consensus       178 ~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p  210 (256)
                      .|||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            456666666666666666666666666666655

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

Probab=98.74  E-value=1.9e-07  Score=76.55  Aligned_cols=205  Identities=13%  Similarity=0.034  Sum_probs=103.2

Q ss_pred             ccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHH
Q 025225            8 RSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILG   82 (256)
Q Consensus         8 ~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~   82 (256)
                      ..++.+.|.+.++.+...+.     +..++.- ...++...+     +.++.........+          ..+...+..
T Consensus        56 ~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l-~~~~~~~~A-----~~~~~~~~~~~~~~----------~~l~~~l~~  119 (280)
T PF13429_consen   56 SLGDYDEAIEAYEKLLASDKANPQDYERLIQL-LQDGDPEEA-----LKLAEKAYERDGDP----------RYLLSALQL  119 (280)
T ss_dssp             ------------------------------------------------------------------------------H-
T ss_pred             cccccccccccccccccccccccccccccccc-ccccccccc-----cccccccccccccc----------chhhHHHHH
Confidence            35667778777777765543     4444433 455556665     66665433222111          112233556


Q ss_pred             hhcCCCcHHHHHHHHHHHhhcc-CCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRL-LKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~-~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      +.+.++.+++. .+++...... ...+..   .+-..+.+.|+.++|++.+++..+..  +-|....+.++..+...|+.
T Consensus       120 ~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--P~~~~~~~~l~~~li~~~~~  196 (280)
T PF13429_consen  120 YYRLGDYDEAE-ELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELD--PDDPDARNALAWLLIDMGDY  196 (280)
T ss_dssp             HHHTT-HHHHH-HHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHH
T ss_pred             HHHHhHHHHHH-HHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHCCCh
Confidence            77888888886 4545544322 223333   35566778999999999999999885  44688899999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          159 NEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +++.++++...+.. ..|...|..+-.+|...|+.++|..+|++..+. -+.|......+...+.+.|+.++|.+
T Consensus       197 ~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~-~p~d~~~~~~~a~~l~~~g~~~~A~~  269 (280)
T PF13429_consen  197 DEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKL-NPDDPLWLLAYADALEQAGRKDEALR  269 (280)
T ss_dssp             HHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH-STT-HHHHHHHHHHHT----------
T ss_pred             HHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccccccccccc-cccccccccccccccccccccccccc
Confidence            99999999887753 456677889999999999999999999998764 13377888899999999999999987

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.71  E-value=2.5e-08  Score=54.05  Aligned_cols=34  Identities=26%  Similarity=0.548  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP  175 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  175 (256)
                      +.|||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            3689999999999999999999999999999988

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.67  E-value=2.8e-06  Score=66.65  Aligned_cols=152  Identities=15%  Similarity=0.095  Sum_probs=105.9

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      +..+...+...|+.++|...+. ......  |+..    .+-..+...|++++|.+.+++..+..  ..+...+..+...
T Consensus        34 ~~~la~~~~~~~~~~~A~~~~~-~~l~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~~~~~  108 (234)
T TIGR02521        34 RVQLALGYLEQGDLEVAKENLD-KALEHD--PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN--PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHH-HHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHH
Confidence            3344566777888888875543 333221  3222    35666777888888888888887765  4566777778888


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCC-CCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          152 LARTGKMNEAMQVWESMRKEDLF-PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~-p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      +...|++++|.+.|++..+.... .+...+..+-..|...|++++|...|.+..+.. ..+...+..+...+...|++++
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHH
Confidence            88888888888888888764222 234566667777888888888888888877653 1235567778888888888888


Q ss_pred             HHH
Q 025225          231 KVK  233 (256)
Q Consensus       231 a~~  233 (256)
                      |.+
T Consensus       188 A~~  190 (234)
T TIGR02521       188 ARA  190 (234)
T ss_pred             HHH
Confidence            877

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.

>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=98.66  E-value=1.7e-06  Score=78.85  Aligned_cols=206  Identities=10%  Similarity=-0.015  Sum_probs=112.4

Q ss_pred             ccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHH
Q 025225            8 RSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILG   82 (256)
Q Consensus         8 ~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~   82 (256)
                      ..|+++.|++.++...+...     |..+-..+...++...+     +..|+......+..         ...+..+-..
T Consensus       343 ~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA-----~~~~~~al~~~p~~---------~~~~~~lg~~  408 (615)
T TIGR00990       343 LKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKA-----EEDFDKALKLNSED---------PDIYYHRAQL  408 (615)
T ss_pred             HcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHHhCCCC---------HHHHHHHHHH
Confidence            35566666666665433221     22222333344444444     55555444332111         1223333445


Q ss_pred             hhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      +...|+.++|+..+ +....  ..|+..    .+-..+.+.|++++|+..|++..+..  .-+...|+.+-..+...|++
T Consensus       409 ~~~~g~~~~A~~~~-~kal~--l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~  483 (615)
T TIGR00990       409 HFIKGEFAQAGKDY-QKSID--LDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF--PEAPDVYNYYGELLLDQNKF  483 (615)
T ss_pred             HHHcCCHHHHHHHH-HHHHH--cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHccCH
Confidence            56677777776433 33322  223322    24555666777777777777776553  44566777777777777777


Q ss_pred             HHHHHHHHHHHhCCCC--C---CH-hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          159 NEAMQVWESMRKEDLF--P---DS-QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~--p---~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ++|.+.|++..+..-.  +   +. ..++.....|...|++++|.+++++..+.. .-+...+..+...+.+.|++++|+
T Consensus       484 ~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~-p~~~~a~~~la~~~~~~g~~~eAi  562 (615)
T TIGR00990       484 DEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIID-PECDIAVATMAQLLLQQGDVDEAL  562 (615)
T ss_pred             HHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHccCHHHHH
Confidence            7777777776653110  1   11 112222233334577777777777766543 123345677777788888887777


Q ss_pred             H
Q 025225          233 K  233 (256)
Q Consensus       233 ~  233 (256)
                      +
T Consensus       563 ~  563 (615)
T TIGR00990       563 K  563 (615)
T ss_pred             H
Confidence            7

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.66  E-value=9e-06  Score=63.74  Aligned_cols=154  Identities=12%  Similarity=0.075  Sum_probs=116.1

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccC-CCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLL-KMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ..+...+...|+.++|...+ +......- .++.. .+-..+...|++++|.+.|++..+..........+..+-..+..
T Consensus        69 ~~la~~~~~~~~~~~A~~~~-~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  147 (234)
T TIGR02521        69 LALALYYQQLGELEKAEDSF-RRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALK  147 (234)
T ss_pred             HHHHHHHHHcCCHHHHHHHH-HHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHH
Confidence            34456777889999998544 44433321 12222 46777888999999999999998754123345677778888999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+.+++..+. ..++...+..+...+...|+.++|..
T Consensus       148 ~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~  224 (234)
T TIGR02521       148 AGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQR  224 (234)
T ss_pred             cCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHH
Confidence            999999999999988742 124567888999999999999999999998876 34466777788888888899888876

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.

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

Probab=98.64  E-value=6.2e-07  Score=61.47  Aligned_cols=76  Identities=18%  Similarity=0.441  Sum_probs=42.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCC-CCCHhhHHHHHHHHHHcC--------ChhHHHHHHHHHHhCCCCCChhHHHHHH
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDL-FPDSQTYTEVIRGFLKDG--------SPADAMNIYEDMIKSPDPPEELPFRILL  219 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~t~~~li~~~~~~g--------~~~~a~~~~~~M~~~g~~p~~~t~~~li  219 (256)
                      |..+...+++.....+|+.+++.|+ .|++.+||.++.+-++..        ++-+.+.+++.|...+++|+..||+++|
T Consensus        32 I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl  111 (120)
T PF08579_consen   32 INSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVL  111 (120)
T ss_pred             HHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHH
Confidence            4444444555555555555555555 555555555555554432        2334556666666666667777776666


Q ss_pred             HHhcC
Q 025225          220 KGLLP  224 (256)
Q Consensus       220 ~~~~~  224 (256)
                      ..+.+
T Consensus       112 ~~Llk  116 (120)
T PF08579_consen  112 GSLLK  116 (120)
T ss_pred             HHHHH
Confidence            66544

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 [, , ].

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

Probab=98.64  E-value=3.4e-08  Score=52.26  Aligned_cols=29  Identities=28%  Similarity=0.618  Sum_probs=17.0

Q ss_pred             hHHHHHHHHHHcCChhHHHHHHHHHHhCC
Q 025225          179 TYTEVIRGFLKDGSPADAMNIYEDMIKSP  207 (256)
Q Consensus       179 t~~~li~~~~~~g~~~~a~~~~~~M~~~g  207 (256)
                      |||+||++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            55555555555555555555555555554

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=98.57  E-value=5.3e-06  Score=75.62  Aligned_cols=226  Identities=13%  Similarity=0.017  Sum_probs=146.6

Q ss_pred             CCchHHHHHHHHHhcCC-C-------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHH
Q 025225           10 KIPILASIVLQNLTKNP-S-------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVIL   81 (256)
Q Consensus        10 ~~~~~A~~l~~~m~~~~-~-------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~   81 (256)
                      +..+.|.+.|+...+.+ .       |+.+-..+...++...+     +..|+......+..         ...+..+..
T Consensus       308 ~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA-----~~~~~kal~l~P~~---------~~~~~~la~  373 (615)
T TIGR00990       308 ESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEA-----LADLSKSIELDPRV---------TQSYIKRAS  373 (615)
T ss_pred             hhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHcCCCc---------HHHHHHHHH
Confidence            45667888888766432 1       33333333445666666     77777665443321         234455566


Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNE  160 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~  160 (256)
                      .+...|+.++|+..+.+......-.|+.. .+-..+...|++++|...|++..+..  ..+...|..+-..+.+.|++++
T Consensus       374 ~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~--P~~~~~~~~la~~~~~~g~~~e  451 (615)
T TIGR00990       374 MNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD--PDFIFSHIQLGVTQYKEGSIAS  451 (615)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--ccCHHHHHHHHHHHHHCCCHHH
Confidence            67788999999865543333222223333 46667788999999999999998875  5567888888889999999999


Q ss_pred             HHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChh------HHHHHHHHhcCCCChHHHHH
Q 025225          161 AMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEEL------PFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       161 a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~------t~~~li~~~~~~g~~~~a~~  233 (256)
                      |...|++..+.  .| +...|+.+-..|...|++++|.+.|++..+..-..+..      .++..+..+...|++++|.+
T Consensus       452 A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~  529 (615)
T TIGR00990       452 SMATFRRCKKN--FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAEN  529 (615)
T ss_pred             HHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHH
Confidence            99999988763  34 46788888999999999999999999877653211111      12222223344688888888


Q ss_pred             hhh--hhcCCCcc-cccchhHhh
Q 025225          234 KDF--EELFPEKH-AYDPPEEIF  253 (256)
Q Consensus       234 ~~~--~~~~p~~~-~~~~li~~y  253 (256)
                      ...  ..+.|+.. .+..+..+|
T Consensus       530 ~~~kAl~l~p~~~~a~~~la~~~  552 (615)
T TIGR00990       530 LCEKALIIDPECDIAVATMAQLL  552 (615)
T ss_pred             HHHHHHhcCCCcHHHHHHHHHHH
Confidence            333  23445433 344454443

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

Probab=98.55  E-value=8e-08  Score=50.79  Aligned_cols=31  Identities=29%  Similarity=0.658  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDL  173 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  173 (256)
                      +|||++|++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4899999999999999999999999999875

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.

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

Probab=98.55  E-value=1.1e-06  Score=60.21  Aligned_cols=79  Identities=16%  Similarity=0.389  Sum_probs=70.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHhcC--------CHHHHHHHHHHHHhCCCCCCHhhHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWY-QPDAYIYKDLIIALARTG--------KMNEAMQVWESMRKEDLFPDSQTYT  181 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~-~p~~~~y~~li~~~~~~g--------~~~~a~~~~~~m~~~g~~p~~~t~~  181 (256)
                      ..|..+...+++.....+|+.+++.| + .|++.+||.++.+.++..        ++-+...+++.|...+++|+..|||
T Consensus        30 ~~I~~~~~~~d~N~I~~lYqslkRN~-i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   30 DNINSCFENEDYNIINPLYQSLKRNG-ITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHhhcchHHHHHHHHHHHhcC-CCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            36667777799999999999999999 8 999999999999998763        4567789999999999999999999


Q ss_pred             HHHHHHHHc
Q 025225          182 EVIRGFLKD  190 (256)
Q Consensus       182 ~li~~~~~~  190 (256)
                      .+|..+.+.
T Consensus       109 ivl~~Llkg  117 (120)
T PF08579_consen  109 IVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHh
Confidence            999998763

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 [, , ].

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

Probab=98.42  E-value=1.9e-06  Score=73.75  Aligned_cols=115  Identities=13%  Similarity=0.155  Sum_probs=101.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDW-YQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK  189 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~-~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  189 (256)
                      .+++.+....+++.+..++...+.... ...-..|..++|..|.+.|..+++.+++..=...|+-||..|||.||+.+.+
T Consensus        71 ~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~  150 (429)
T PF10037_consen   71 IFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLK  150 (429)
T ss_pred             HHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhh
Confidence            688888888899999999999887731 2233345579999999999999999999998888999999999999999999


Q ss_pred             cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          190 DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       190 ~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                      .|++..|.++...|...+...+..|+...+.+|.+.
T Consensus       151 ~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  151 KGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             cccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999999999999999988888999999888888877

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 [].

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.36  E-value=2.6e-05  Score=76.09  Aligned_cols=148  Identities=14%  Similarity=0.094  Sum_probs=114.0

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      .....+...|+.++|.. +++   ...-.|... .+-..+.+.|+.++|+..|+...+..  +.++..+..+...|...|
T Consensus       578 ~~a~~l~~~G~~~eA~~-~l~---~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~--P~~~~a~~~la~~~~~~g  651 (1157)
T PRK11447        578 ETANRLRDSGKEAEAEA-LLR---QQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE--PGNADARLGLIEVDIAQG  651 (1157)
T ss_pred             HHHHHHHHCCCHHHHHH-HHH---hCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCC
Confidence            34566788999999974 433   111122222 57777889999999999999999886  567889999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC--CC---ChhHHHHHHHHhcCCCChHH
Q 025225          157 KMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD--PP---EELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~--~p---~~~t~~~li~~~~~~g~~~~  230 (256)
                      +.++|.+.++...+.  .|+ ..++..+-..+.+.|++++|.+++++.....-  .|   +...+..+.+.+...|+.++
T Consensus       652 ~~~eA~~~l~~ll~~--~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~  729 (1157)
T PRK11447        652 DLAAARAQLAKLPAT--ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQ  729 (1157)
T ss_pred             CHHHHHHHHHHHhcc--CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHH
Confidence            999999999987763  343 45566777888899999999999999886532  22   23456666788889999999


Q ss_pred             HHH
Q 025225          231 KVK  233 (256)
Q Consensus       231 a~~  233 (256)
                      |+.
T Consensus       730 A~~  732 (1157)
T PRK11447        730 ALE  732 (1157)
T ss_pred             HHH
Confidence            988

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

Probab=98.27  E-value=6.8e-05  Score=65.91  Aligned_cols=217  Identities=11%  Similarity=0.046  Sum_probs=152.8

Q ss_pred             ccccCCchHHHHHHHHH-hcCCC----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNL-TKNPS----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m-~~~~~----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      |...+++|.|..-++.. ..++-    +.-+-..|-.+|.++-+     +..|++.....+..         ...+..+-
T Consensus       262 ~ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlA-----I~~Ykral~~~P~F---------~~Ay~Nla  327 (966)
T KOG4626|consen  262 YKEARIFDRAVSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLA-----IDTYKRALELQPNF---------PDAYNNLA  327 (966)
T ss_pred             HHHHhcchHHHHHHHHHHhcCCcchhhccceEEEEeccccHHHH-----HHHHHHHHhcCCCc---------hHHHhHHH
Confidence            44555666665555442 22221    44444455566777767     88887776665544         45566667


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhc-cCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLR-LLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      +++...|++.++.+ .+...... .--+|.. .|=+.+...|.+++|..+|..-.+-.  .--...+|.|-..|-..|++
T Consensus       328 nALkd~G~V~ea~~-cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~--p~~aaa~nNLa~i~kqqgnl  404 (966)
T KOG4626|consen  328 NALKDKGSVTEAVD-CYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVF--PEFAAAHNNLASIYKQQGNL  404 (966)
T ss_pred             HHHHhccchHHHHH-HHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhC--hhhhhhhhhHHHHHHhcccH
Confidence            88888899999974 43333321 1122222 48888889999999999999877653  44567889999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-hhHHHHHHHHhcCCCChHHHHH--h
Q 025225          159 NEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-ELPFRILLKGLLPHPLLRSKVK--K  234 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~--~  234 (256)
                      ++|...+++..+  +.|+- ..|+.+=..|-..|+++.|.+.+.+-.+.+  |. ...++.|-..|-..|.+.+|+.  .
T Consensus       405 ~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~n--Pt~AeAhsNLasi~kDsGni~~AI~sY~  480 (966)
T KOG4626|consen  405 DDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQIN--PTFAEAHSNLASIYKDSGNIPEAIQSYR  480 (966)
T ss_pred             HHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcC--cHHHHHHhhHHHHhhccCCcHHHHHHHH
Confidence            999999998776  66774 678888888888999999999998876653  33 2456788889999999999988  4


Q ss_pred             hhhhcCCCc
Q 025225          235 DFEELFPEK  243 (256)
Q Consensus       235 ~~~~~~p~~  243 (256)
                      ..-.+.||.
T Consensus       481 ~aLklkPDf  489 (966)
T KOG4626|consen  481 TALKLKPDF  489 (966)
T ss_pred             HHHccCCCC
Confidence            455666764

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.25  E-value=7.7e-05  Score=64.38  Aligned_cols=225  Identities=9%  Similarity=-0.022  Sum_probs=126.6

Q ss_pred             cCCchHHHHHHHHHhcCC---C--ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHh
Q 025225            9 SKIPILASIVLQNLTKNP---S--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGL   83 (256)
Q Consensus         9 ~~~~~~A~~l~~~m~~~~---~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~   83 (256)
                      .|+.+.|.+.+..-.+.+   .  |-..-.+..+.++.+.+     ...+.++.+..+...        -.........+
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A-----~~~l~~A~~~~~~~~--------~~~~l~~a~l~  163 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARA-----NQHLERAAELADNDQ--------LPVEITRVRIQ  163 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHhcCCcch--------HHHHHHHHHHH
Confidence            477777777777655432   2  22222232455666666     667766654332220        01111113455


Q ss_pred             hcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCC-----------------------
Q 025225           84 KRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWY-----------------------  138 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~-----------------------  138 (256)
                      ...|+.++|.. .++...+.. -.|... .+...|.+.|++++|.+++..+.+.+..                       
T Consensus       164 l~~g~~~~Al~-~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~  242 (398)
T PRK10747        164 LARNENHAARH-GVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMAD  242 (398)
T ss_pred             HHCCCHHHHHH-HHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            67788888874 334444333 112222 4777788888888888888887766511                       


Q ss_pred             -----------------CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHH
Q 025225          139 -----------------QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYE  201 (256)
Q Consensus       139 -----------------~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~  201 (256)
                                       +.++.....+..++...|+.++|.+++++..+.  .||..  -.++.+.+..++.+++.+..+
T Consensus       243 ~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~--l~~l~~~l~~~~~~~al~~~e  318 (398)
T PRK10747        243 QGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER--LVLLIPRLKTNNPEQLEKVLR  318 (398)
T ss_pred             cCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH--HHHHHhhccCCChHHHHHHHH
Confidence                             123334445566666778888888888877763  33431  112333344567777777777


Q ss_pred             HHHhCCCCCCh-hHHHHHHHHhcCCCChHHHHH--hhhhhcCCCcccccchhHhh
Q 025225          202 DMIKSPDPPEE-LPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYDPPEEIF  253 (256)
Q Consensus       202 ~M~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~~li~~y  253 (256)
                      +..+.  .|+. ..+.++-+.|.+.|++++|.+  ...-...|+..+|-.+..++
T Consensus       319 ~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~  371 (398)
T PRK10747        319 QQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADAL  371 (398)
T ss_pred             HHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            66654  2333 345566777777777777777  33344567666655555544

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.24  E-value=0.00015  Score=68.94  Aligned_cols=201  Identities=10%  Similarity=0.023  Sum_probs=139.2

Q ss_pred             CCchHHHHHHHHHh-cCCC-cccccccc--CCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhc
Q 025225           10 KIPILASIVLQNLT-KNPS-KNFSFLAF--KPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKR   85 (256)
Q Consensus        10 ~~~~~A~~l~~~m~-~~~~-~~~ll~a~--~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~   85 (256)
                      +++++|...+.... ..+- ++-+..++  ...++...+     +..|+++....+.+          ..+......+.+
T Consensus       490 ~~~~eAi~a~~~Al~~~Pd~~~~L~lA~al~~~Gr~eeA-----i~~~rka~~~~p~~----------~a~~~la~all~  554 (987)
T PRK09782        490 TLPGVALYAWLQAEQRQPDAWQHRAVAYQAYQVEDYATA-----LAAWQKISLHDMSN----------EDLLAAANTAQA  554 (987)
T ss_pred             CCcHHHHHHHHHHHHhCCchHHHHHHHHHHHHCCCHHHH-----HHHHHHHhccCCCc----------HHHHHHHHHHHH
Confidence            56777877555533 3332 33222222  356666666     77777654332211          223344556778


Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHHH----HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIVA----VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEA  161 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~~----li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a  161 (256)
                      .|+.++|.. +++......  |+...    +.......|++++|...+.+..+..   |+...|..+-..+.+.|+.++|
T Consensus       555 ~Gd~~eA~~-~l~qAL~l~--P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~---P~~~a~~~LA~~l~~lG~~deA  628 (987)
T PRK09782        555 AGNGAARDR-WLQQAEQRG--LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA---PSANAYVARATIYRQRHNVPAA  628 (987)
T ss_pred             CCCHHHHHH-HHHHHHhcC--CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC---CCHHHHHHHHHHHHHCCCHHHH
Confidence            899999874 445554433  44432    2233345599999999999988664   6788999999999999999999


Q ss_pred             HHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          162 MQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       162 ~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      ...|++..+.  .|+ ...++.+-..+...|+.++|.+.|++..+... -+...+..+-..+...|++++|...
T Consensus       629 ~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P-~~~~a~~nLA~al~~lGd~~eA~~~  699 (987)
T PRK09782        629 VSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLP-DDPALIRQLAYVNQRLDDMAATQHY  699 (987)
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            9999998874  464 45666777789999999999999998887522 2556778889999999999999883

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

Probab=98.21  E-value=4.3e-05  Score=64.73  Aligned_cols=197  Identities=10%  Similarity=0.052  Sum_probs=147.3

Q ss_pred             ccCCchHHHHHHHHHhcCCC------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHH
Q 025225            8 RSKIPILASIVLQNLTKNPS------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVIL   81 (256)
Q Consensus         8 ~~~~~~~A~~l~~~m~~~~~------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~   81 (256)
                      ..|+.+.|.+.+.+..+.+.      ||+-+ .+...++++++     +.+|-.++.-....         ......+.+
T Consensus       502 ~ngd~dka~~~ykeal~ndasc~ealfnigl-t~e~~~~ldea-----ld~f~klh~il~nn---------~evl~qian  566 (840)
T KOG2003|consen  502 ANGDLDKAAEFYKEALNNDASCTEALFNIGL-TAEALGNLDEA-----LDCFLKLHAILLNN---------AEVLVQIAN  566 (840)
T ss_pred             ecCcHHHHHHHHHHHHcCchHHHHHHHHhcc-cHHHhcCHHHH-----HHHHHHHHHHHHhh---------HHHHHHHHH
Confidence            36888999999998766553      88877 34556778888     88885544221110         112233456


Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      .|-...+..+|++.+   |....+.|+--    .|-..|-+.|+-.+|++.+-+--+-  +.-+..|..-|-.-|....-
T Consensus       567 iye~led~aqaie~~---~q~~slip~dp~ilskl~dlydqegdksqafq~~ydsyry--fp~nie~iewl~ayyidtqf  641 (840)
T KOG2003|consen  567 IYELLEDPAQAIELL---MQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY--FPCNIETIEWLAAYYIDTQF  641 (840)
T ss_pred             HHHHhhCHHHHHHHH---HHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc--cCcchHHHHHHHHHHHhhHH
Confidence            667777888887433   55556666433    3667777899999999998876655  56788888888889999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH-cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCC
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK-DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPL  227 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~-~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~  227 (256)
                      +++|...|++..-  ++|+..-|..||..|.+ .|++++|+++++..... +.-|.....-|++.+...|.
T Consensus       642 ~ekai~y~ekaal--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  642 SEKAINYFEKAAL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHHHHHHh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccc
Confidence            9999999997543  67999999999998875 79999999999987654 66688888899999998885

>PRK12370 invasion protein regulator; Provisional

Probab=98.21  E-value=0.00018  Score=64.85  Aligned_cols=140  Identities=12%  Similarity=-0.030  Sum_probs=99.9

Q ss_pred             CCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 025225           87 KDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAM  162 (256)
Q Consensus        87 ~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~  162 (256)
                      ++.++|...+ +...+  +.|+..    .+=..+...|++++|...|++..+.+  +.+...|..+-..|...|++++|.
T Consensus       318 ~~~~~A~~~~-~~Al~--ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~G~~~eAi  392 (553)
T PRK12370        318 NAMIKAKEHA-IKATE--LDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS--PISADIKYYYGWNLFMAGQLEEAL  392 (553)
T ss_pred             hHHHHHHHHH-HHHHh--cCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            3456676433 33333  234322    24445667899999999999998886  556778888888999999999999


Q ss_pred             HHHHHHHhCCCCCCHh-hHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCChHHHHHh
Q 025225          163 QVWESMRKEDLFPDSQ-TYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       163 ~~~~~m~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      ..+++..+.  .|+.. .+..+...+...|++++|...+++..+.. .| +...+..+-..|...|+.++|...
T Consensus       393 ~~~~~Al~l--~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~  463 (553)
T PRK12370        393 QTINECLKL--DPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKL  463 (553)
T ss_pred             HHHHHHHhc--CCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHH
Confidence            999998874  35432 23344445667899999999999987653 24 344466777788899999999883

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.18  E-value=3.4e-05  Score=66.56  Aligned_cols=216  Identities=13%  Similarity=0.042  Sum_probs=130.4

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEAL   77 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~   77 (256)
                      .+-+.|+++.|.+.++.+.+...       .-..  .+.+.++...+     +.++..+.+.....+. ....+....+.
T Consensus       162 l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~--~~~~~gdw~~a-----~~~l~~l~k~~~~~~~-~~~~l~~~a~~  233 (398)
T PRK10747        162 IQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQ--AYIRTGAWSSL-----LDILPSMAKAHVGDEE-HRAMLEQQAWI  233 (398)
T ss_pred             HHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHH--HHHHHHhHHHH-----HHHHHHHHHcCCCCHH-HHHHHHHHHHH
Confidence            45567888888888887755432       2111  12344666666     7777777766544322 11211112222


Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhc-cCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLR-LLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      .++.......+ .+.+..+++...+. .-.|... ++..++...|+.++|.+++.+..+..   ||..  -.++.+....
T Consensus       234 ~l~~~~~~~~~-~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~---~~~~--l~~l~~~l~~  307 (398)
T PRK10747        234 GLMDQAMADQG-SEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQ---YDER--LVLLIPRLKT  307 (398)
T ss_pred             HHHHHHHHhcC-HHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC---CCHH--HHHHHhhccC
Confidence            22222222222 23333444333211 1112222 57888888888888888888877643   4441  1123444455


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          156 GKMNEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      ++.+++.+..++..+.  .||. ..+-++=..|.+.|++++|.+.|+...+.  .|+..+|..+-..+.+.|+.++|.+.
T Consensus       308 ~~~~~al~~~e~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~  383 (398)
T PRK10747        308 NNPEQLEKVLRQQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAM  383 (398)
T ss_pred             CChHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            8888888888887764  3544 45667777888888888999888888876  58888888888888888888888774


Q ss_pred             hhhh
Q 025225          235 DFEE  238 (256)
Q Consensus       235 ~~~~  238 (256)
                      -..+
T Consensus       384 ~~~~  387 (398)
T PRK10747        384 RRDG  387 (398)
T ss_pred             HHHH
Confidence            3333

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

Probab=98.16  E-value=8.6e-05  Score=60.32  Aligned_cols=212  Identities=10%  Similarity=0.022  Sum_probs=140.6

Q ss_pred             cCCchHHHHHHHHHhcCCC----ccccc-cccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHh
Q 025225            9 SKIPILASIVLQNLTKNPS----KNFSF-LAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGL   83 (256)
Q Consensus         9 ~~~~~~A~~l~~~m~~~~~----~~~ll-~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~   83 (256)
                      +.+||.|.++|.+|.+...    -+..+ +-+.+.|.++.+     +++.+.+..+...+   .-..+  -....+-..|
T Consensus        48 s~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRA-----IRiHQ~L~~spdlT---~~qr~--lAl~qL~~Dy  117 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRA-----IRIHQTLLESPDLT---FEQRL--LALQQLGRDY  117 (389)
T ss_pred             hcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHH-----HHHHHHHhcCCCCc---hHHHH--HHHHHHHHHH
Confidence            6789999999999976543    23333 334556777778     88887666443222   11111  1223345667


Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH----HHHHHHHHHHHhcCCH
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDA----YIYKDLIIALARTGKM  158 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~y~~li~~~~~~g~~  158 (256)
                      -..|-.+.|-+.|...+.+....++.. .|+..|-..++|++|.++-.++.+.++ .+..    ..|.-|-..+....++
T Consensus       118 m~aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~-q~~~~eIAqfyCELAq~~~~~~~~  196 (389)
T COG2956         118 MAAGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGG-QTYRVEIAQFYCELAQQALASSDV  196 (389)
T ss_pred             HHhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCC-ccchhHHHHHHHHHHHHHhhhhhH
Confidence            778888888655544444444555544 599999999999999999998887762 2221    1233333344456788


Q ss_pred             HHHHHHHHHHHhCCCCCCHhhHHHHH-HHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          159 NEAMQVWESMRKEDLFPDSQTYTEVI-RGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~~t~~~li-~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++|..++.+..+.+  |+.+--++++ +-+...|+++.|.+.++...+.+..--+.+...|..+|.+.|+.+++..
T Consensus       197 d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~  270 (389)
T COG2956         197 DRARELLKKALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLN  270 (389)
T ss_pred             HHHHHHHHHHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            88888888877642  4443333333 3455788899999999988888776667778888889999988887766

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.12  E-value=0.0004  Score=66.17  Aligned_cols=145  Identities=11%  Similarity=0.036  Sum_probs=88.6

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCC-cHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKM-DIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAM  162 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~  162 (256)
                      ...|+.++|+..+ +........+ ....+-.++.+.|++++|.+.+++..+..  ..+...+..+.....+.|++++|.
T Consensus       520 ~~~Gr~eeAi~~~-rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~--P~~~~l~~~La~~l~~~Gr~~eAl  596 (987)
T PRK09782        520 YQVEDYATALAAW-QKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG--LGDNALYWWLHAQRYIPGQPELAL  596 (987)
T ss_pred             HHCCCHHHHHHHH-HHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHhCCCHHHHH
Confidence            4667777776443 3332211111 11134455666777777777777776654  233333333333444557888888


Q ss_pred             HHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          163 QVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       163 ~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      ..|++..+.  .|+...|..+-..+.+.|+.++|...|++..+.. .-+...++.+-..+...|+.++|+..
T Consensus       597 ~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~  665 (987)
T PRK09782        597 NDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREM  665 (987)
T ss_pred             HHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            888777653  4677777777778888888888888888776652 12344555666677788888887773

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.12  E-value=0.00012  Score=71.64  Aligned_cols=204  Identities=11%  Similarity=0.003  Sum_probs=144.1

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +...|+.++|++.++...+...     +..+-..+...++...+     +..+++.....+..+         .......
T Consensus       471 ~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A-----~~~l~~al~~~P~~~---------~~~~a~a  536 (1157)
T PRK11447        471 LENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQA-----DALMRRLAQQKPNDP---------EQVYAYG  536 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHcCCCCH---------HHHHHHH
Confidence            3457888999999998754332     33444556677777777     888887765433221         1111122


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH------------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV------------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDL  148 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~------------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~l  148 (256)
                      ..+...++.++|+.. ++........++..            .+.+.+...|+.++|.++++    .  ...+...+..+
T Consensus       537 l~l~~~~~~~~Al~~-l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~----~--~p~~~~~~~~L  609 (1157)
T PRK11447        537 LYLSGSDRDRAALAH-LNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLR----Q--QPPSTRIDLTL  609 (1157)
T ss_pred             HHHHhCCCHHHHHHH-HHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHH----h--CCCCchHHHHH
Confidence            234567888888743 34433222222221            34567888999999999987    2  25566778889


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCC
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPL  227 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~  227 (256)
                      -..|.+.|+.++|.+.|++..+.. +.+...+..+...|...|+.++|.+.++...+.  .| +..++..+-..+...|+
T Consensus       610 a~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~--~p~~~~~~~~la~~~~~~g~  686 (1157)
T PRK11447        610 ADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPAT--ANDSLNTQRRVALAWAALGD  686 (1157)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCChHHHHHHHHHHHhCCC
Confidence            999999999999999999998852 235788999999999999999999999987754  33 34556677888889999


Q ss_pred             hHHHHH
Q 025225          228 LRSKVK  233 (256)
Q Consensus       228 ~~~a~~  233 (256)
                      +++|.+
T Consensus       687 ~~eA~~  692 (1157)
T PRK11447        687 TAAAQR  692 (1157)
T ss_pred             HHHHHH
Confidence            999998

>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=98.10  E-value=4.8e-05  Score=58.62  Aligned_cols=81  Identities=14%  Similarity=0.235  Sum_probs=56.7

Q ss_pred             HHHHHHHH-----cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc----------------CCHHHHHHHHHHHH
Q 025225          111 AVLIELER-----QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART----------------GKMNEAMQVWESMR  169 (256)
Q Consensus       111 ~li~~~~~-----~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~----------------g~~~~a~~~~~~m~  169 (256)
                      .+|+.|.+     .|.++=....+..|.+.| +.-|..+|+.||+.+=+.                .+-+-|.+++++|.
T Consensus        52 ~~V~~f~~~~~~RRGHVeFI~aAL~~M~efg-v~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME  130 (228)
T PF06239_consen   52 EAVDIFKQRDVRRRGHVEFIYAALKKMDEFG-VEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQME  130 (228)
T ss_pred             HHHHHHHhcCCCCcChHHHHHHHHHHHHHcC-CcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHHHH
Confidence            47777764     367788888888888888 888888888888887652                23455666666666


Q ss_pred             hCCCCCCHhhHHHHHHHHHHcCC
Q 025225          170 KEDLFPDSQTYTEVIRGFLKDGS  192 (256)
Q Consensus       170 ~~g~~p~~~t~~~li~~~~~~g~  192 (256)
                      ..|+.||..|+..|++.+++.+.
T Consensus       131 ~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  131 NNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HcCCCCcHHHHHHHHHHhccccH
Confidence            66666666666666666655554

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

>PRK12370 invasion protein regulator; Provisional

Probab=98.09  E-value=0.00047  Score=62.18  Aligned_cols=161  Identities=10%  Similarity=-0.055  Sum_probs=107.1

Q ss_pred             cccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHH
Q 025225           50 ILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILA  125 (256)
Q Consensus        50 ~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a  125 (256)
                      +..+++.....+..         ...+..+-..+...|+.++|...+ +...+.  .|+..    .+-..+...|++++|
T Consensus       324 ~~~~~~Al~ldP~~---------~~a~~~lg~~~~~~g~~~~A~~~~-~~Al~l--~P~~~~a~~~lg~~l~~~G~~~eA  391 (553)
T PRK12370        324 KEHAIKATELDHNN---------PQALGLLGLINTIHSEYIVGSLLF-KQANLL--SPISADIKYYYGWNLFMAGQLEEA  391 (553)
T ss_pred             HHHHHHHHhcCCCC---------HHHHHHHHHHHHHccCHHHHHHHH-HHHHHh--CCCCHHHHHHHHHHHHHCCCHHHH
Confidence            66666555443322         222333344566789999998555 444333  34432    366678889999999


Q ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          126 VKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       126 ~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      ...+++..+..  +.+...+..+...+...|++++|...+++..+.. .|+ ...+..+-..|...|+.++|.+.+.++.
T Consensus       392 i~~~~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~  468 (553)
T PRK12370        392 LQTINECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEIS  468 (553)
T ss_pred             HHHHHHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhh
Confidence            99999998876  2233344445556777899999999999987643 244 4446677778889999999999999876


Q ss_pred             hCCCCCChh-HHHHHHHHhcCCCC
Q 025225          205 KSPDPPEEL-PFRILLKGLLPHPL  227 (256)
Q Consensus       205 ~~g~~p~~~-t~~~li~~~~~~g~  227 (256)
                      ..  .|+.. -.+.+...|+..|+
T Consensus       469 ~~--~~~~~~~~~~l~~~~~~~g~  490 (553)
T PRK12370        469 TQ--EITGLIAVNLLYAEYCQNSE  490 (553)
T ss_pred             hc--cchhHHHHHHHHHHHhccHH
Confidence            55  34433 34455556777774

>TIGR00540 hemY_coli hemY protein

Probab=98.08  E-value=9.4e-05  Score=64.11  Aligned_cols=123  Identities=11%  Similarity=0.007  Sum_probs=90.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHH---HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHh---hHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYI---YKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQ---TYTEVI  184 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~---y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~---t~~~li  184 (256)
                      .+...+...|+.++|.+++++..+..   ||...   ...........++.+++.+.+++..+.  .|+..   ...++=
T Consensus       268 ~~a~~l~~~g~~~~A~~~l~~~l~~~---pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~--~p~~~~~~ll~sLg  342 (409)
T TIGR00540       268 ALAEHLIDCDDHDSAQEIIFDGLKKL---GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN--VDDKPKCCINRALG  342 (409)
T ss_pred             HHHHHHHHCCChHHHHHHHHHHHhhC---CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh--CCCChhHHHHHHHH
Confidence            47788889999999999999988774   33321   122222223457888888888887764  35544   445777


Q ss_pred             HHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhhhh
Q 025225          185 RGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEE  238 (256)
Q Consensus       185 ~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~  238 (256)
                      ..|.+.|++++|.+.|+.-......|+...+..+...+.+.|+.++|.+...++
T Consensus       343 ~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       343 QLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            788899999999999996555555789999999999999999999888744443

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.

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

Probab=98.06  E-value=0.0001  Score=64.84  Aligned_cols=156  Identities=14%  Similarity=0.136  Sum_probs=102.7

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+=+-|...+.++.|+..+.+..   ...|+..    .+--.|...|+++.|+..|++..+..  .--...||.|-.++-
T Consensus       257 NLGnV~ke~~~~d~Avs~Y~rAl---~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~--P~F~~Ay~NlanALk  331 (966)
T KOG4626|consen  257 NLGNVYKEARIFDRAVSCYLRAL---NLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQ--PNFPDAYNNLANALK  331 (966)
T ss_pred             hHHHHHHHHhcchHHHHHHHHHH---hcCCcchhhccceEEEEeccccHHHHHHHHHHHHhcC--CCchHHHhHHHHHHH
Confidence            33344445555555554333322   2333322    13334567788888888888877664  334568888888888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-hhHHHHHHHHhcCCCChHHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-ELPFRILLKGLLPHPLLRSK  231 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-~~t~~~li~~~~~~g~~~~a  231 (256)
                      ..|++.+|++.+++....  .|+ ....+.|-..|..-|++++|..+|..-.+-  .|. ...+|.|-..|-+.|++++|
T Consensus       332 d~G~V~ea~~cYnkaL~l--~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~A  407 (966)
T KOG4626|consen  332 DKGSVTEAVDCYNKALRL--CPNHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDA  407 (966)
T ss_pred             hccchHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHH
Confidence            888888888888887763  344 356777888888888888888888876654  222 34567777788888888888


Q ss_pred             HH--hhhhhcCCC
Q 025225          232 VK--KDFEELFPE  242 (256)
Q Consensus       232 ~~--~~~~~~~p~  242 (256)
                      +.  .+.-.|.|.
T Consensus       408 i~~YkealrI~P~  420 (966)
T KOG4626|consen  408 IMCYKEALRIKPT  420 (966)
T ss_pred             HHHHHHHHhcCch
Confidence            77  455556654

>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=98.06  E-value=0.00025  Score=60.60  Aligned_cols=115  Identities=17%  Similarity=0.150  Sum_probs=97.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      +|++.+...++++.|.++|+++.+..   |++  .-.+...+...++-.+|.+++++..+. .+-|....+.-.+.|.+.
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~~~---pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k  247 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRERD---PEV--AVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSK  247 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHhcC---CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhc
Confidence            48888888999999999999999774   554  445888888899999999999988864 223667777777788899


Q ss_pred             CChhHHHHHHHHHHhCCCCCChh-HHHHHHHHhcCCCChHHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEEL-PFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++.+.|..+.+++.+.  .|+.. +|..|..+|.+.|++++|+.
T Consensus       248 ~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALl  289 (395)
T PF09295_consen  248 KKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALL  289 (395)
T ss_pred             CCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHH
Confidence            9999999999998876  56655 99999999999999999987

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

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

Probab=98.06  E-value=3.9e-06  Score=75.90  Aligned_cols=90  Identities=16%  Similarity=0.225  Sum_probs=62.3

Q ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC
Q 025225          128 IFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP  207 (256)
Q Consensus       128 ~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g  207 (256)
                      ++..+...| +.|+.+||..+|.-||..|+.+.|- +|.-|+-.....+...|+.++.+...+++.+.+.          
T Consensus        12 fla~~e~~g-i~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk----------   79 (1088)
T KOG4318|consen   12 FLALHEISG-ILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK----------   79 (1088)
T ss_pred             HHHHHHHhc-CCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC----------
Confidence            455666666 6777777777777777777777777 7777766666666677777777777777665554          


Q ss_pred             CCCChhHHHHHHHHhcCCCChHH
Q 025225          208 DPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       208 ~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                       .|...||..|+.+|..+|++.-
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~  101 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLIL  101 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHH
Confidence             5667777777777777776553

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

Probab=98.05  E-value=0.00015  Score=60.30  Aligned_cols=184  Identities=16%  Similarity=0.106  Sum_probs=106.9

Q ss_pred             ccccccccCCchHHHHHHHHHhcCCC-------------ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccc
Q 025225            2 ATRLFSRSKIPILASIVLQNLTKNPS-------------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRG   68 (256)
Q Consensus         2 ~i~~~~~~~~~~~A~~l~~~m~~~~~-------------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~   68 (256)
                      |.+.|-+.|..+....++.+|.+.+.             |+.++.=+...+..++-     ....+...... +.     
T Consensus       193 a~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL-----~~~W~~~pr~l-r~-----  261 (400)
T COG3071         193 ALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGL-----KTWWKNQPRKL-RN-----  261 (400)
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHH-----HHHHHhccHHh-hc-----
Confidence            45667778888888888888888775             44444333333322221     11121111111 00     


Q ss_pred             ccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 025225           69 KKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDL  148 (256)
Q Consensus        69 ~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~l  148 (256)
                         ...-....+.-+.+.|+.++|. .+..+..++...|...+++ .+.+-++.+.=.+..+...+..  +-++..+-+|
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 ---DPELVVAYAERLIRLGDHDEAQ-EIIEDALKRQWDPRLCRLI-PRLRPGDPEPLIKAAEKWLKQH--PEDPLLLSTL  334 (400)
T ss_pred             ---ChhHHHHHHHHHHHcCChHHHH-HHHHHHHHhccChhHHHHH-hhcCCCCchHHHHHHHHHHHhC--CCChhHHHHH
Confidence               0112223355666777777776 4445566666666533333 3344555555555555444443  2233667777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      =..|.+.+.+.+|.+.|+.-.+  ..|+..+|+-+-.+|.+.|++++|.+++++-..
T Consensus       335 G~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~  389 (400)
T COG3071         335 GRLALKNKLWGKASEALEAALK--LRPSASDYAELADALDQLGEPEEAEQVRREALL  389 (400)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            7777778888888888875444  457788888888888888888888777776553

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

Probab=97.99  E-value=7.1e-05  Score=64.22  Aligned_cols=110  Identities=14%  Similarity=0.203  Sum_probs=93.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHH
Q 025225          138 YQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE--DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPF  215 (256)
Q Consensus       138 ~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~  215 (256)
                      ...+......+++.+....+++++..++.+....  ....-..|.+++|+.|.+.|..+++++++..=..-|+=||..||
T Consensus        62 ~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   62 KPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            4678889999999999999999999999999875  33334456689999999999999999999998999999999999


Q ss_pred             HHHHHHhcCCCChHHHHH----hhhhhcCCCccccc
Q 025225          216 RILLKGLLPHPLLRSKVK----KDFEELFPEKHAYD  247 (256)
Q Consensus       216 ~~li~~~~~~g~~~~a~~----~~~~~~~p~~~~~~  247 (256)
                      |.|++.+.+.|++..|++    |...+...++.|+.
T Consensus       142 n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~  177 (429)
T PF10037_consen  142 NLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQA  177 (429)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHH
Confidence            999999999999999998    44455555555554

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 [].

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

Probab=97.94  E-value=0.00066  Score=56.63  Aligned_cols=149  Identities=15%  Similarity=0.051  Sum_probs=84.0

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      ...|.+.|++.+.+ .+...+.+.++-.+..          .+++-....+..+.-...+++..+.  .+.++..-.+++
T Consensus       194 ~r~y~~~g~~~~ll-~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~--lr~~p~l~~~~a  270 (400)
T COG3071         194 LRAYIRLGAWQALL-AILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK--LRNDPELVVAYA  270 (400)
T ss_pred             HHHHHHhccHHHHH-HHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH--hhcChhHHHHHH
Confidence            45556666666654 3445555555443332          1223322223333323333333333  244455555566


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCC------------------------------HhhHHHHHHHHHHcCChhHHHHH
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFPD------------------------------SQTYTEVIRGFLKDGSPADAMNI  199 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p~------------------------------~~t~~~li~~~~~~g~~~~a~~~  199 (256)
                      .-+..+|+.++|.++.++-.+++..|+                              .-.+.+|=.-|.+.+.+.+|.+.
T Consensus       271 ~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~  350 (400)
T COG3071         271 ERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEA  350 (400)
T ss_pred             HHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHH
Confidence            666666666666666655554443333                              23456666667778888888888


Q ss_pred             HHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          200 YEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       200 ~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |+.-.  ..+|+..+|+.+-+.+.+.|+..+|-+
T Consensus       351 leaAl--~~~~s~~~~~~la~~~~~~g~~~~A~~  382 (400)
T COG3071         351 LEAAL--KLRPSASDYAELADALDQLGEPEEAEQ  382 (400)
T ss_pred             HHHHH--hcCCChhhHHHHHHHHHHcCChHHHHH
Confidence            87433  346788888888888888887777665

>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=97.93  E-value=8.2e-05  Score=57.36  Aligned_cols=89  Identities=16%  Similarity=0.184  Sum_probs=75.0

Q ss_pred             CCHHHHHHHHHHHH-----hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc----------------CChhHHHH
Q 025225          140 PDAYIYKDLIIALA-----RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD----------------GSPADAMN  198 (256)
Q Consensus       140 p~~~~y~~li~~~~-----~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~----------------g~~~~a~~  198 (256)
                      .|-.+|..+|..|.     +.|.++=....+..|.+-|+.-|..+|+.||+.+=+.                .+-+-|.+
T Consensus        45 k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~  124 (228)
T PF06239_consen   45 KDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAID  124 (228)
T ss_pred             ccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHH
Confidence            46666666666665     3488999999999999999999999999999986552                23566999


Q ss_pred             HHHHHHhCCCCCChhHHHHHHHHhcCCCCh
Q 025225          199 IYEDMIKSPDPPEELPFRILLKGLLPHPLL  228 (256)
Q Consensus       199 ~~~~M~~~g~~p~~~t~~~li~~~~~~g~~  228 (256)
                      +++.|...|+.||..|+..|++.+++.+.-
T Consensus       125 lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  125 LLEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence            999999999999999999999999998843

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

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.93  E-value=0.0023  Score=53.01  Aligned_cols=120  Identities=17%  Similarity=0.060  Sum_probs=58.3

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN  159 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~  159 (256)
                      ..+.+.|+.++|...+.+......-.|+.. .+=..+...|++++|.+.|+...+..  .-+..+|..+-..+...|+++
T Consensus        72 ~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~g~~~  149 (296)
T PRK11189         72 VLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAYLNRGIALYYGGRYE  149 (296)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHH
Confidence            345556666666544432222111111111 24445556666666666666666543  234455555666666666666


Q ss_pred             HHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          160 EAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +|.+.|++..+.  .|+..........+...++.++|.+.|.+..
T Consensus       150 eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        150 LAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            666666665552  2433211111111223455666666665433

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.91  E-value=0.0016  Score=61.07  Aligned_cols=160  Identities=11%  Similarity=-0.028  Sum_probs=111.7

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccC-CCcHH--HHHHHHHHcCCHHHHHHHHHHHHhcCCCCC--CHHHHHHHHHHHHhcC
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLL-KMDIV--AVLIELERQEETILAVKIFDIIRKQDWYQP--DAYIYKDLIIALARTG  156 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~p--~~~~y~~li~~~~~~g  156 (256)
                      .+...++.++|+..+ +.+.+.+- .|+..  .+-.++...|++++|+..|++..+.....+  ....+..+..++...|
T Consensus       246 ~Ll~~g~~~eA~~~~-~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g  324 (765)
T PRK10049        246 ALLARDRYKDVISEY-QRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESE  324 (765)
T ss_pred             HHHHhhhHHHHHHHH-HHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcc
Confidence            345668888888555 55655542 25432  356678889999999999999876541111  1355677777889999


Q ss_pred             CHHHHHHHHHHHHhCC-----------CCCC---HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          157 KMNEAMQVWESMRKED-----------LFPD---SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g-----------~~p~---~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      ++++|.++++++.+..           -.|+   ...+..+...+...|+.++|.++++++... -+-+...+..+...+
T Consensus       325 ~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~-~P~n~~l~~~lA~l~  403 (765)
T PRK10049        325 NYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYN-APGNQGLRIDYASVL  403 (765)
T ss_pred             cHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHH
Confidence            9999999999988642           1123   124456777888899999999999998765 233456777888888


Q ss_pred             cCCCChHHHHHh--hhhhcCCCc
Q 025225          223 LPHPLLRSKVKK--DFEELFPEK  243 (256)
Q Consensus       223 ~~~g~~~~a~~~--~~~~~~p~~  243 (256)
                      ...|+.++|.+.  ....+.||.
T Consensus       404 ~~~g~~~~A~~~l~~al~l~Pd~  426 (765)
T PRK10049        404 QARGWPRAAENELKKAEVLEPRN  426 (765)
T ss_pred             HhcCCHHHHHHHHHHHHhhCCCC
Confidence            889999888883  334445664

>TIGR00540 hemY_coli hemY protein

Probab=97.88  E-value=0.0012  Score=57.32  Aligned_cols=158  Identities=15%  Similarity=0.023  Sum_probs=101.3

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcH--H-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDI--V-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ..-..+.+.|+.+++.. ++....+..-.+..  . +.-..+...|++++|.+.++.+.+..  +-+...+..+...|..
T Consensus       123 laA~aa~~~g~~~~A~~-~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~--P~~~~~l~ll~~~~~~  199 (409)
T TIGR00540       123 KAAEAAQQRGDEARANQ-HLEEAAELAGNDNILVEIARTRILLAQNELHAARHGVDKLLEMA--PRHKEVLKLAEEAYIR  199 (409)
T ss_pred             HHHHHHHHCCCHHHHHH-HHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHH
Confidence            33456677888888864 44444332222222  1 35667778999999999999999886  4567788899999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH---HHcCChhHHHHHHHHHHhCCC---CCChhHHHHHHHHhcCCCCh
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGF---LKDGSPADAMNIYEDMIKSPD---PPEELPFRILLKGLLPHPLL  228 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~---~~~g~~~~a~~~~~~M~~~g~---~p~~~t~~~li~~~~~~g~~  228 (256)
                      .|++++|.+++.++.+.+..++...-..-..++   ...+..+++.+.+..+.+...   +.+...+-.+...+...|+.
T Consensus       200 ~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~  279 (409)
T TIGR00540       200 SGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDH  279 (409)
T ss_pred             HhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCCh
Confidence            999999999999999876543222211111211   222333333445555444321   23677778888888888888


Q ss_pred             HHHHHhhhhh
Q 025225          229 RSKVKKDFEE  238 (256)
Q Consensus       229 ~~a~~~~~~~  238 (256)
                      ++|.+...+.
T Consensus       280 ~~A~~~l~~~  289 (409)
T TIGR00540       280 DSAQEIIFDG  289 (409)
T ss_pred             HHHHHHHHHH
Confidence            8888844333

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.

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

Probab=97.87  E-value=0.00057  Score=55.69  Aligned_cols=185  Identities=12%  Similarity=-0.013  Sum_probs=127.5

Q ss_pred             cccccCCchHHHHHHHHHhcCCC--cc-------ccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchh
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS--KN-------FSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKE   75 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~--~~-------~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~   75 (256)
                      .|-+.|..|.|+.+-+.+.+++.  ++       -+-.-|-..|-++.+     ..+|..+.+.+...         ...
T Consensus        78 LfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRA-----E~~f~~L~de~efa---------~~A  143 (389)
T COG2956          78 LFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRA-----EDIFNQLVDEGEFA---------EGA  143 (389)
T ss_pred             HHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHH-----HHHHHHHhcchhhh---------HHH
Confidence            46678999999999999887765  11       122233445666667     88888777644322         233


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHH-------HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIE-------LERQEETILAVKIFDIIRKQDWYQPDAYIYKDL  148 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~-------~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~l  148 (256)
                      .-.++..|-...++++|++.- ....+.+-.+...-+-..       .....+++.|...+..-.+..  +..+..--.+
T Consensus       144 lqqLl~IYQ~treW~KAId~A-~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~--~~cvRAsi~l  220 (389)
T COG2956         144 LQQLLNIYQATREWEKAIDVA-ERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQAD--KKCVRASIIL  220 (389)
T ss_pred             HHHHHHHHHHhhHHHHHHHHH-HHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhC--ccceehhhhh
Confidence            345678888999999998544 445555544544433333       334567888998888877665  3333333344


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      =+.+...|++++|.+.++...+.+..--..+...|..+|.+.|+.++...++.++.+.
T Consensus       221 G~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         221 GRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             hHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            4566788999999999999888654444567788999999999999999999888765

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

Probab=97.85  E-value=0.00098  Score=48.03  Aligned_cols=102  Identities=19%  Similarity=0.211  Sum_probs=80.6

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+...+...|+.++|.+.|+...+.+  ..+...|..+-..|.+.|++++|...|++..+.+ ..+...|..+-..|...
T Consensus        22 ~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~   98 (135)
T TIGR02552        22 ALAYNLYQQGRYDEALKLFQLLAAYD--PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLAL   98 (135)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHc
Confidence            36667778899999999999988876  5688888889999999999999999999877653 33566677777788889


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRI  217 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~  217 (256)
                      |+.++|...|++..+.  .|+...+..
T Consensus        99 g~~~~A~~~~~~al~~--~p~~~~~~~  123 (135)
T TIGR02552        99 GEPESALKALDLAIEI--CGENPEYSE  123 (135)
T ss_pred             CCHHHHHHHHHHHHHh--ccccchHHH
Confidence            9999999999887775  355555443

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

>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=97.84  E-value=0.00024  Score=58.44  Aligned_cols=136  Identities=18%  Similarity=0.147  Sum_probs=76.4

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHHH-HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cC
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIVA-VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TG  156 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g  156 (256)
                      .+...|+.++|+..+     ..+-.+...+ .+..+.+.++++.|.+.++.|++..   .| .+-..+..++..    .+
T Consensus       111 i~~~~~~~~~AL~~l-----~~~~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~---eD-~~l~qLa~awv~l~~g~e  181 (290)
T PF04733_consen  111 ILFHEGDYEEALKLL-----HKGGSLELLALAVQILLKMNRPDLAEKELKNMQQID---ED-SILTQLAEAWVNLATGGE  181 (290)
T ss_dssp             HHCCCCHHHHHHCCC-----TTTTCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS---CC-HHHHHHHHHHHHHHHTTT
T ss_pred             HHHHcCCHHHHHHHH-----HccCcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC---Cc-HHHHHHHHHHHHHHhCch
Confidence            445566666666322     1222223332 5677777777777777777777554   23 333334444433    34


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCCh
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLL  228 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~  228 (256)
                      .+.+|..+|+++.+. ..++..+.|.+..++...|++++|.+++.+..+..- -+..|...++.+....|+-
T Consensus       182 ~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-~~~d~LaNliv~~~~~gk~  251 (290)
T PF04733_consen  182 KYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-NDPDTLANLIVCSLHLGKP  251 (290)
T ss_dssp             CCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHTT-T
T ss_pred             hHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCC
Confidence            577777777776553 456677777777777777777777777777554432 2344555566666666655

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=97.82  E-value=0.0028  Score=59.45  Aligned_cols=162  Identities=15%  Similarity=0.099  Sum_probs=122.4

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCC-CcHH--HHHHHHHHcCCHHHHHHHHHHHHhcC----CCCCCHHHHHHHHHH
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLK-MDIV--AVLIELERQEETILAVKIFDIIRKQD----WYQPDAYIYKDLIIA  151 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~----~~~p~~~~y~~li~~  151 (256)
                      .+.++...++..++++.+ +.+...+.+ |+..  ++-++|...+++++|+.+|.......    ...++......|.-+
T Consensus       298 rl~aL~~r~r~~~vi~~y-~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA  376 (822)
T PRK14574        298 RLGALLVRHQTADLIKEY-EAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYS  376 (822)
T ss_pred             HHHHHHHhhhHHHHHHHH-HHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHH
Confidence            367788899999998655 677777754 6655  69999999999999999999986542    023455557889999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCC-------------CCCCHhh-HHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHH
Q 025225          152 LARTGKMNEAMQVWESMRKED-------------LFPDSQT-YTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRI  217 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g-------------~~p~~~t-~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~  217 (256)
                      |...+++++|..+++++.+..             -.||-.. +..++..+...|++.+|++.++++... -+-|......
T Consensus       377 ~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~-aP~n~~l~~~  455 (822)
T PRK14574        377 LNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSST-APANQNLRIA  455 (822)
T ss_pred             HHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHH
Confidence            999999999999999998731             1122222 345677788899999999999999765 2447777888


Q ss_pred             HHHHhcCCCChHHHHHh--hhhhcCCC
Q 025225          218 LLKGLLPHPLLRSKVKK--DFEELFPE  242 (256)
Q Consensus       218 li~~~~~~g~~~~a~~~--~~~~~~p~  242 (256)
                      +-+.+...|..++|.+.  ....+.|+
T Consensus       456 ~A~v~~~Rg~p~~A~~~~k~a~~l~P~  482 (822)
T PRK14574        456 LASIYLARDLPRKAEQELKAVESLAPR  482 (822)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHhhhCCc
Confidence            88899999999988883  33344555

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.81  E-value=0.0041  Score=49.41  Aligned_cols=157  Identities=18%  Similarity=0.168  Sum_probs=107.4

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcH----HHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH-HHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDI----VAVLIELERQEETILAVKIFDIIRKQDWYQPDA-YIYKDLI  149 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~y~~li  149 (256)
                      ........+.+.|+.++|...+.+......-.|..    ..+-.++...|++++|...++++.+..+-.|.. .++..+-
T Consensus        35 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g  114 (235)
T TIGR03302        35 ELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRG  114 (235)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHH
Confidence            44455667888999999986554333322222211    136678889999999999999998775112221 1344444


Q ss_pred             HHHHhc--------CCHHHHHHHHHHHHhCCCCCCHh-hHH-----------------HHHHHHHHcCChhHHHHHHHHH
Q 025225          150 IALART--------GKMNEAMQVWESMRKEDLFPDSQ-TYT-----------------EVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       150 ~~~~~~--------g~~~~a~~~~~~m~~~g~~p~~~-t~~-----------------~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      .++...        |+.++|.+.|++..+.  .|+.. .+.                 .+-..|.+.|++++|...+.+.
T Consensus       115 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~a  192 (235)
T TIGR03302       115 LSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETV  192 (235)
T ss_pred             HHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            444443        7899999999998874  34432 211                 3345677889999999999998


Q ss_pred             HhCC--CCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          204 IKSP--DPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       204 ~~~g--~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .+..  -......+..+...+.+.|++++|..
T Consensus       193 l~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~  224 (235)
T TIGR03302       193 VENYPDTPATEEALARLVEAYLKLGLKDLAQD  224 (235)
T ss_pred             HHHCCCCcchHHHHHHHHHHHHHcCCHHHHHH
Confidence            8662  22345688899999999999999988

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).

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

Probab=97.80  E-value=0.0025  Score=54.50  Aligned_cols=120  Identities=13%  Similarity=0.139  Sum_probs=98.1

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      .++..+...++.+.|+ .+++.+.+..  |+.. .+.+.+...++-.+|.++.++..+..  +-|......-...+.+.+
T Consensus       174 ~Ll~~l~~t~~~~~ai-~lle~L~~~~--pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~--p~d~~LL~~Qa~fLl~k~  248 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAI-ELLEKLRERD--PEVAVLLARVYLLMNEEVEAIRLLNEALKEN--PQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHhhcccHHHHH-HHHHHHHhcC--CcHHHHHHHHHHhcCcHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhcC
Confidence            3455566678899988 4556666555  7766 46777777888899999999988774  567788888888899999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +.+.|.++.+++.+  +.|+. .+|..|...|.+.|+++.|+-.++.+.
T Consensus       249 ~~~lAL~iAk~av~--lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  249 KYELALEIAKKAVE--LSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CHHHHHHHHHHHHH--hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            99999999999887  45765 599999999999999999999999876

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

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.79  E-value=0.0027  Score=59.56  Aligned_cols=155  Identities=12%  Similarity=0.092  Sum_probs=94.9

Q ss_pred             hhcCCCcHHHHHHHHHHHhhccCC-CcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRLLK-MDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEA  161 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a  161 (256)
                      ..+.|+..+|++.+.+........ |.+..++..+...|+.++|+..+++.....  .........+...|...|++++|
T Consensus        44 ~~r~Gd~~~Al~~L~qaL~~~P~~~~av~dll~l~~~~G~~~~A~~~~eka~~p~--n~~~~~llalA~ly~~~gdyd~A  121 (822)
T PRK14574         44 RARAGDTAPVLDYLQEESKAGPLQSGQVDDWLQIAGWAGRDQEVIDVYERYQSSM--NISSRGLASAARAYRNEKRWDQA  121 (822)
T ss_pred             HHhCCCHHHHHHHHHHHHhhCccchhhHHHHHHHHHHcCCcHHHHHHHHHhccCC--CCCHHHHHHHHHHHHHcCCHHHH
Confidence            367888888876554433322222 123356777777788888888888777221  33344444445677777888888


Q ss_pred             HHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhh
Q 025225          162 MQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEE  238 (256)
Q Consensus       162 ~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~  238 (256)
                      .++|+++.+..  | |...+..++..|.+.++.++|++.+++....  .|+...+-.++..+...++..+|++  ...-.
T Consensus       122 iely~kaL~~d--P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~  197 (822)
T PRK14574        122 LALWQSSLKKD--PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVR  197 (822)
T ss_pred             HHHHHHHHhhC--CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHH
Confidence            88888887742  3 2455567777788888888888888887766  4555555444333333444444655  23333


Q ss_pred             cCCCc
Q 025225          239 LFPEK  243 (256)
Q Consensus       239 ~~p~~  243 (256)
                      ..|+.
T Consensus       198 ~~P~n  202 (822)
T PRK14574        198 LAPTS  202 (822)
T ss_pred             hCCCC
Confidence            44543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.77  E-value=0.0021  Score=47.23  Aligned_cols=100  Identities=12%  Similarity=-0.018  Sum_probs=82.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      ..-..+...|++++|...|+......  ..+...|..+-..+...|++++|...|++....+ ..+...+..+-.++.+.
T Consensus        29 ~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~  105 (144)
T PRK15359         29 ASGYASWQEGDYSRAVIDFSWLVMAQ--PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMM  105 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHc
Confidence            45566778999999999999998886  6788899999999999999999999999988742 23678888888889999


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPF  215 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~  215 (256)
                      |+.++|...|++-.+.  .|+...|
T Consensus       106 g~~~eAi~~~~~Al~~--~p~~~~~  128 (144)
T PRK15359        106 GEPGLAREAFQTAIKM--SYADASW  128 (144)
T ss_pred             CCHHHHHHHHHHHHHh--CCCChHH
Confidence            9999999999988765  3444333

>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=97.77  E-value=0.00032  Score=57.73  Aligned_cols=125  Identities=14%  Similarity=0.048  Sum_probs=86.0

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----cC
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----DG  191 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g  191 (256)
                      +...|++++|+++++.-       .+....-..+..|.+.+++|.|.+.++.|++.  ..| .+-..|..++..    .+
T Consensus       112 ~~~~~~~~~AL~~l~~~-------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~eD-~~l~qLa~awv~l~~g~e  181 (290)
T PF04733_consen  112 LFHEGDYEEALKLLHKG-------GSLELLALAVQILLKMNRPDLAEKELKNMQQI--DED-SILTQLAEAWVNLATGGE  181 (290)
T ss_dssp             HCCCCHHHHHHCCCTTT-------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--SCC-HHHHHHHHHHHHHHHTTT
T ss_pred             HHHcCCHHHHHHHHHcc-------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCc-HHHHHHHHHHHHHHhCch
Confidence            34568899888887642       35677777888899999999999999998874  234 444445555554    33


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhhhhcCCCcccccchhH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEE  251 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~p~~~~~~~li~  251 (256)
                      ++++|..+|+++.+. ..+++.+.|.+..+....|++++|.+.....+.-|+.-.+++++
T Consensus       182 ~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaN  240 (290)
T PF04733_consen  182 KYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLAN  240 (290)
T ss_dssp             CCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHH
T ss_pred             hHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHH
Confidence            688999999997665 56788888889999999999999888544445444444445444

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.

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

Probab=97.76  E-value=0.00034  Score=61.81  Aligned_cols=206  Identities=13%  Similarity=0.009  Sum_probs=125.2

Q ss_pred             HHHHHHHHhcCCC-ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHH
Q 025225           15 ASIVLQNLTKNPS-KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKL   93 (256)
Q Consensus        15 A~~l~~~m~~~~~-~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~   93 (256)
                      |.+|++..+.++- |..+=..|+-+++.+.+     ++.|++...-.+..         ...++-+=+.+......++|.
T Consensus       410 aq~Li~~~~~sPesWca~GNcfSLQkdh~~A-----ik~f~RAiQldp~f---------aYayTLlGhE~~~~ee~d~a~  475 (638)
T KOG1126|consen  410 AQDLIDTDPNSPESWCALGNCFSLQKDHDTA-----IKCFKRAIQLDPRF---------AYAYTLLGHESIATEEFDKAM  475 (638)
T ss_pred             HHHHHhhCCCCcHHHHHhcchhhhhhHHHHH-----HHHHHHhhccCCcc---------chhhhhcCChhhhhHHHHhHH
Confidence            4445555544443 66666666666666666     77776554333222         111111112223333444443


Q ss_pred             HHHHHHHhhccCCCcHH-H---HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225           94 QKFIKTHVLRLLKMDIV-A---VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus        94 ~~~~~~~~~~~~~~~~~-~---li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      ..| +..  -++-|..+ +   +--.|.|.++++.|+-.|+...+.+  .-+.+.-..+-..+-+.|+.|+|.++|++..
T Consensus       476 ~~f-r~A--l~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN--P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~  550 (638)
T KOG1126|consen  476 KSF-RKA--LGVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN--PSNSVILCHIGRIQHQLKRKDKALQLYEKAI  550 (638)
T ss_pred             HHH-Hhh--hcCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCC--ccchhHHhhhhHHHHHhhhhhHHHHHHHHHH
Confidence            222 111  23334443 2   6666778889999999999888776  5677777777778888899999999999887


Q ss_pred             hCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-hhHHHHHHHHhcCCCChHHHHH--hhhhhcCCC
Q 025225          170 KEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-ELPFRILLKGLLPHPLLRSKVK--KDFEELFPE  242 (256)
Q Consensus       170 ~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~  242 (256)
                      ...-+ |..+--.-...+...++.++|+..++++++.  .|+ ...|-.+-+.|-+.|..+.|+.  -...++.|-
T Consensus       551 ~ld~k-n~l~~~~~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpk  623 (638)
T KOG1126|consen  551 HLDPK-NPLCKYHRASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPK  623 (638)
T ss_pred             hcCCC-CchhHHHHHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCc
Confidence            64332 3333233344455578889999999998876  444 4455667778888888888877  333444443

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.74  E-value=0.0043  Score=58.24  Aligned_cols=148  Identities=12%  Similarity=0.126  Sum_probs=111.6

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhh-ccCCCc-HHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVL-RLLKMD-IVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~-~~~~~~-~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      +......|+.++|+..+ ..... ...... ...+-.++.+.|++++|.++|++..+..  +.+...+..+...+...|+
T Consensus        22 ~~ia~~~g~~~~A~~~~-~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~l~~~g~   98 (765)
T PRK10049         22 LQIALWAGQDAEVITVY-NRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE--PQNDDYQRGLILTLADAGQ   98 (765)
T ss_pred             HHHHHHcCCHHHHHHHH-HHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCC
Confidence            34456889999998444 44443 222111 1257778889999999999999988774  5567778889999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +++|...+++..+.  .|+...+..+-..+...|+.++|...+++..+.... +...+..+...+...|..++|++
T Consensus        99 ~~eA~~~l~~~l~~--~P~~~~~~~la~~l~~~g~~~~Al~~l~~al~~~P~-~~~~~~~la~~l~~~~~~e~Al~  171 (765)
T PRK10049         99 YDEALVKAKQLVSG--APDKANLLALAYVYKRAGRHWDELRAMTQALPRAPQ-TQQYPTEYVQALRNNRLSAPALG  171 (765)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCChHHHHH
Confidence            99999999999875  354333888888899999999999999999887322 33444567777778888887776

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

Probab=97.71  E-value=0.0011  Score=43.32  Aligned_cols=92  Identities=20%  Similarity=0.240  Sum_probs=67.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +...+...|++++|...+++..+..  ..+...+..+...+...|++++|.+.|++..+.. ..+..++..+...+...|
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   82 (100)
T cd00189           6 LGNLYYKLGDYDEALEYYEKALELD--PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLG   82 (100)
T ss_pred             HHHHHHHHhcHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHH
Confidence            4455667788888888888887664  4455677778888888888888888888876643 223357777778888888


Q ss_pred             ChhHHHHHHHHHHhC
Q 025225          192 SPADAMNIYEDMIKS  206 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~  206 (256)
                      +.++|...+.+..+.
T Consensus        83 ~~~~a~~~~~~~~~~   97 (100)
T cd00189          83 KYEEALEAYEKALEL   97 (100)
T ss_pred             hHHHHHHHHHHHHcc
Confidence            888888888776543

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

Probab=97.65  E-value=0.0024  Score=56.65  Aligned_cols=215  Identities=12%  Similarity=0.075  Sum_probs=140.1

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .+.+.|+.++|...+..+.+.+.     |..+..+..-...+..........+|.++...-++......-          
T Consensus        47 ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl----------  116 (517)
T PF12569_consen   47 LLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRL----------  116 (517)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccchhHh----------
Confidence            35567888888888888766554     555554442222212212222366776665554443222211          


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHHH-HHHHHHHcCCHHHHHHHHHHHHhc----CC---------CCCCHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVA-VLIELERQEETILAVKIFDIIRKQ----DW---------YQPDAYIY  145 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-li~~~~~~~~~~~a~~~~~~m~~~----~~---------~~p~~~~y  145 (256)
                      .-.+.....+...++.++..+..+|+ |+..+ |-..|.......-..+++......    +.         -.|++..|
T Consensus       117 ~L~~~~g~~F~~~~~~yl~~~l~Kgv-PslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw  195 (517)
T PF12569_consen  117 PLDFLEGDEFKERLDEYLRPQLRKGV-PSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLW  195 (517)
T ss_pred             hcccCCHHHHHHHHHHHHHHHHhcCC-chHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHH
Confidence            12233345566677788888888887 66665 444444444555555666555422    11         23555555


Q ss_pred             H--HHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          146 K--DLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       146 ~--~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      .  -+-..|-..|++++|.+..++..+.  .|+ +..|..--+-|-+.|++++|.+.++.-++... -|...=+-....+
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~-~DRyiNsK~aKy~  272 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELDL-ADRYINSKCAKYL  272 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCh-hhHHHHHHHHHHH
Confidence            4  4456677899999999999988875  476 56677778888899999999999998886632 2667777888889


Q ss_pred             cCCCChHHHHH
Q 025225          223 LPHPLLRSKVK  233 (256)
Q Consensus       223 ~~~g~~~~a~~  233 (256)
                      .++|++++|.+
T Consensus       273 LRa~~~e~A~~  283 (517)
T PF12569_consen  273 LRAGRIEEAEK  283 (517)
T ss_pred             HHCCCHHHHHH
Confidence            99999999988

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 [], [].

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

Probab=97.64  E-value=0.0021  Score=46.29  Aligned_cols=115  Identities=17%  Similarity=0.128  Sum_probs=86.2

Q ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC
Q 025225          128 IFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP  207 (256)
Q Consensus       128 ~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g  207 (256)
                      .++...+..  ..+......+...+...|++++|.+.|++....+ ..+...|..+-..|.+.|++++|..++++..+.+
T Consensus         5 ~~~~~l~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~   81 (135)
T TIGR02552         5 TLKDLLGLD--SEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD   81 (135)
T ss_pred             hHHHHHcCC--hhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            344555443  3345667777888899999999999999987753 2367788888889999999999999999887764


Q ss_pred             CCCChhHHHHHHHHhcCCCChHHHHHhhh--hhcCCCcccc
Q 025225          208 DPPEELPFRILLKGLLPHPLLRSKVKKDF--EELFPEKHAY  246 (256)
Q Consensus       208 ~~p~~~t~~~li~~~~~~g~~~~a~~~~~--~~~~p~~~~~  246 (256)
                       ..+..++..+-..|...|++++|++...  ....|+...+
T Consensus        82 -p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~  121 (135)
T TIGR02552        82 -PDDPRPYFHAAECLLALGEPESALKALDLAIEICGENPEY  121 (135)
T ss_pred             -CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchH
Confidence             4456777778889999999999988333  3344555443

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

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

Probab=97.62  E-value=0.0087  Score=46.45  Aligned_cols=110  Identities=6%  Similarity=0.095  Sum_probs=54.8

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHH-HHHcCC--hh
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRG-FLKDGS--PA  194 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~-~~~~g~--~~  194 (256)
                      .++.+++...+....+..  ..|...|..+-..|...|++++|...|++..+..  | |...+..+-.+ |...|+  .+
T Consensus        52 ~~~~~~~i~~l~~~L~~~--P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~--P~~~~~~~~lA~aL~~~~g~~~~~  127 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLR--GENAELYAALATVLYYQAGQHMTP  127 (198)
T ss_pred             chhHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCCCcH
Confidence            444455555555544443  4455555555555555555555555555555422  3 33444444433 234444  35


Q ss_pred             HHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          195 DAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       195 ~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +|.+++++..+.... +...+..+-..+.+.|++++|+.
T Consensus       128 ~A~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~  165 (198)
T PRK10370        128 QTREMIDKALALDAN-EVTALMLLASDAFMQADYAQAIE  165 (198)
T ss_pred             HHHHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHH
Confidence            555555555544221 33444555555555555555555

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.60  E-value=0.017  Score=47.79  Aligned_cols=142  Identities=15%  Similarity=0.042  Sum_probs=93.7

Q ss_pred             CCcHHHHHHHHHHHhhccCCCcHH-----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 025225           87 KDDEEKLQKFIKTHVLRLLKMDIV-----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEA  161 (256)
Q Consensus        87 ~~~~~a~~~~~~~~~~~~~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a  161 (256)
                      +..+.++..+.+........|+..     .+=..+.+.|+.++|...|++..+..  ..+...|+.+-..|...|++++|
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~~~~~g~~~~A  117 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR--PDMADAYNYLGIYLTQAGNFDAA  117 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHCCCHHHH
Confidence            344555545544343334444432     23345677888888888888888775  55678888888888888888888


Q ss_pred             HHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          162 MQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       162 ~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      .+.|++..+.  .|+ ...|..+-..+...|++++|.+.|++-.+.  .|+..........+...++.++|...
T Consensus       118 ~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~  187 (296)
T PRK11189        118 YEAFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKEN  187 (296)
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHH
Confidence            8888888763  354 566777777778888888888888887765  34332222222223345677777773

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

Probab=97.55  E-value=0.0079  Score=47.95  Aligned_cols=113  Identities=15%  Similarity=0.123  Sum_probs=60.9

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHH
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFL  188 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  188 (256)
                      +..+.+..+++-|.+-.++|.+-.    +..|.+.|-.+|.+    .+.+.+|.-+|++|.++ ..|+..+-|-...++.
T Consensus       144 VqI~lk~~r~d~A~~~lk~mq~id----ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l  218 (299)
T KOG3081|consen  144 VQILLKMHRFDLAEKELKKMQQID----EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHL  218 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccc----hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHH
Confidence            333445556666666666666443    45555545444443    34566666666666543 3466666666666666


Q ss_pred             HcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHH
Q 025225          189 KDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSK  231 (256)
Q Consensus       189 ~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a  231 (256)
                      ..|++++|..++++.....-+ ++.|...+|-+-...|.-.+.
T Consensus       219 ~~~~~eeAe~lL~eaL~kd~~-dpetL~Nliv~a~~~Gkd~~~  260 (299)
T KOG3081|consen  219 QLGRYEEAESLLEEALDKDAK-DPETLANLIVLALHLGKDAEV  260 (299)
T ss_pred             HhcCHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHHhCCChHH
Confidence            666666666666666544211 233444444444444443333

>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=97.52  E-value=0.0019  Score=46.09  Aligned_cols=84  Identities=21%  Similarity=0.340  Sum_probs=60.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHH---------------hCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMR---------------KEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~---------------~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      |..++.++|-++++.|+++....+.+..=               ...+.||..+..+++.+|+..|++..|+++.+...+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            34566677777777777777766665431               124568888888888888888888888888888765


Q ss_pred             C-CCCCChhHHHHHHHHhcC
Q 025225          206 S-PDPPEELPFRILLKGLLP  224 (256)
Q Consensus       206 ~-g~~p~~~t~~~li~~~~~  224 (256)
                      . ++..+..+|..|++=+..
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v  100 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYV  100 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHH
Confidence            4 777778888888774443

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

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

Probab=97.50  E-value=0.0072  Score=46.90  Aligned_cols=104  Identities=10%  Similarity=0.112  Sum_probs=83.3

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH-HHhcCC--HHHHHHHHHHHHhCCCCC-CHhhHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA-LARTGK--MNEAMQVWESMRKEDLFP-DSQTYTEVIRGF  187 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~-~~~~g~--~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~  187 (256)
                      +-..|...|++++|...|+...+..  .-+...+..+-.+ |...|+  .++|.+++++..+.+  | +...+..+-..+
T Consensus        79 Lg~~~~~~g~~~~A~~a~~~Al~l~--P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d--P~~~~al~~LA~~~  154 (198)
T PRK10370         79 LGEYYLWRNDYDNALLAYRQALQLR--GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD--ANEVTALMLLASDA  154 (198)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC--CCChhHHHHHHHHH
Confidence            5667889999999999999999886  5577888888776 467777  599999999998853  4 567888888889


Q ss_pred             HHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHH
Q 025225          188 LKDGSPADAMNIYEDMIKSPDPPEELPFRILLKG  221 (256)
Q Consensus       188 ~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~  221 (256)
                      .+.|++++|...|+++.+.. .|+..-+. +|++
T Consensus       155 ~~~g~~~~Ai~~~~~aL~l~-~~~~~r~~-~i~~  186 (198)
T PRK10370        155 FMQADYAQAIELWQKVLDLN-SPRVNRTQ-LVES  186 (198)
T ss_pred             HHcCCHHHHHHHHHHHHhhC-CCCccHHH-HHHH
Confidence            99999999999999998773 44544444 3354

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

Probab=97.50  E-value=0.0071  Score=51.74  Aligned_cols=165  Identities=15%  Similarity=0.187  Sum_probs=115.7

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      .+-..|+.++|++.|++..   ++-.+..    .+-+.|-...+..+|.+++-+..+.  +.-|+....-|-..|-+.|+
T Consensus       533 t~e~~~~ldeald~f~klh---~il~nn~evl~qianiye~led~aqaie~~~q~~sl--ip~dp~ilskl~dlydqegd  607 (840)
T KOG2003|consen  533 TAEALGNLDEALDCFLKLH---AILLNNAEVLVQIANIYELLEDPAQAIELLMQANSL--IPNDPAILSKLADLYDQEGD  607 (840)
T ss_pred             cHHHhcCHHHHHHHHHHHH---HHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc--CCCCHHHHHHHHHHhhcccc
Confidence            3456788888887665432   2212222    3556677777888888888776655  56778888889999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhc-CCCChHHHHH--h
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLL-PHPLLRSKVK--K  234 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~-~~g~~~~a~~--~  234 (256)
                      -..|.+.+-+--+ =++-|..|..-|-.-|....-+++|..+|++..  =++|+..-|..||..|. +.|.+.+|++  .
T Consensus       608 ksqafq~~ydsyr-yfp~nie~iewl~ayyidtqf~ekai~y~ekaa--liqp~~~kwqlmiasc~rrsgnyqka~d~yk  684 (840)
T KOG2003|consen  608 KSQAFQCHYDSYR-YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--LIQPNQSKWQLMIASCFRRSGNYQKAFDLYK  684 (840)
T ss_pred             hhhhhhhhhhccc-ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--hcCccHHHHHHHHHHHHHhcccHHHHHHHHH
Confidence            9988887665322 244477777778888888888899999998744  45899999998887655 7899999998  3


Q ss_pred             hhhhcCC-CcccccchhHhhc
Q 025225          235 DFEELFP-EKHAYDPPEEIFG  254 (256)
Q Consensus       235 ~~~~~~p-~~~~~~~li~~y~  254 (256)
                      ..++-.| |.....-|+.+.|
T Consensus       685 ~~hrkfpedldclkflvri~~  705 (840)
T KOG2003|consen  685 DIHRKFPEDLDCLKFLVRIAG  705 (840)
T ss_pred             HHHHhCccchHHHHHHHHHhc
Confidence            3333344 4445555665554

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

Probab=97.49  E-value=0.0014  Score=53.74  Aligned_cols=142  Identities=16%  Similarity=0.166  Sum_probs=98.2

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhc-cCCCcHHH--HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLR-LLKMDIVA--VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~--li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      .|...+...-+.+..+.|-..| ....+. .+..+++.  ..--+...++.+.|..||+...+.  +..+...|..-|+.
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF-~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~--f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVF-KRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK--FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH--HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHH-HHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHH
Confidence            4666677777777777776544 444433 33445441  222344457778899999988877  57788889999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCH----hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhc
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDS----QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLL  223 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~  223 (256)
                      +.+.|+.+.|..+|++.... + |..    ..|...|+-=.+.|+++.+..+.+++.+.  .|+..+...+++-|.
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l-~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry~  151 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-L-PKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRYS  151 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-S-SCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT-
T ss_pred             HHHhCcHHHHHHHHHHHHHh-c-CchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHhh
Confidence            99999999999999988765 3 333    48999999999999999999999988875  555566666666654

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.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.49  E-value=0.0075  Score=42.01  Aligned_cols=96  Identities=14%  Similarity=0.034  Sum_probs=67.4

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCCHhhHHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWY-QPDAYIYKDLIIALARTGKMNEAMQVWESMRKED--LFPDSQTYTEVIRGF  187 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~-~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~t~~~li~~~  187 (256)
                      .+...+.+.|++++|.+.|+.+.+..+- ......+..+...+.+.|++++|.+.|++.....  -......+..+-..+
T Consensus         7 ~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~   86 (119)
T TIGR02795         7 DAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSL   86 (119)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHH
Confidence            4566677788888888888888765311 1113456667888888888888888888877632  111234566677777


Q ss_pred             HHcCChhHHHHHHHHHHhC
Q 025225          188 LKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       188 ~~~g~~~~a~~~~~~M~~~  206 (256)
                      .+.|+.++|...+++..+.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        87 QELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHhCChHHHHHHHHHHHHH
Confidence            8888888888888888776

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.

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

Probab=97.48  E-value=0.017  Score=45.87  Aligned_cols=121  Identities=15%  Similarity=0.042  Sum_probs=98.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      ......+.|++..|...|.+...-.  .+|..+||.+=-+|.+.|++++|..-|.+..+.-. -+...+|.|--.|.-.|
T Consensus       106 ~gk~~~~~g~~~~A~~~~rkA~~l~--p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~-~~p~~~nNlgms~~L~g  182 (257)
T COG5010         106 QGKNQIRNGNFGEAVSVLRKAARLA--PTDWEAWNLLGAALDQLGRFDEARRAYRQALELAP-NEPSIANNLGMSLLLRG  182 (257)
T ss_pred             HHHHHHHhcchHHHHHHHHHHhccC--CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhcc-CCchhhhhHHHHHHHcC
Confidence            5566678899999999999999886  89999999999999999999999999999888422 13455677777777789


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhh
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDF  236 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~  236 (256)
                      +.++|..++.+-...+.. |...-..+.......|++++|-....
T Consensus       183 d~~~A~~lll~a~l~~~a-d~~v~~NLAl~~~~~g~~~~A~~i~~  226 (257)
T COG5010         183 DLEDAETLLLPAYLSPAA-DSRVRQNLALVVGLQGDFREAEDIAV  226 (257)
T ss_pred             CHHHHHHHHHHHHhCCCC-chHHHHHHHHHHhhcCChHHHHhhcc
Confidence            999999999998877544 44555567778888999999887433

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

Probab=97.46  E-value=0.0051  Score=52.64  Aligned_cols=147  Identities=16%  Similarity=0.048  Sum_probs=113.5

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HH-HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AV-LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~l-i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      +=|+-.++.++|+ .+++...+-+-+.... || =+-|....+...|.+-+....+..  +.|-..|=.|=.+|.-.+..
T Consensus       338 NYYSlr~eHEKAv-~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~--p~DyRAWYGLGQaYeim~Mh  414 (559)
T KOG1155|consen  338 NYYSLRSEHEKAV-MYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN--PRDYRAWYGLGQAYEIMKMH  414 (559)
T ss_pred             hHHHHHHhHHHHH-HHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC--chhHHHHhhhhHHHHHhcch
Confidence            3445567778887 4555554433221111 54 466888888999999999888885  78888999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          159 NEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .-|.-.|++..+  ++| |...|.+|=..|.+.++.++|...|.+-...|=. +...+..|-+.|-+.++..+|..
T Consensus       415 ~YaLyYfqkA~~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~LakLye~l~d~~eAa~  487 (559)
T KOG1155|consen  415 FYALYYFQKALE--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAKLYEELKDLNEAAQ  487 (559)
T ss_pred             HHHHHHHHHHHh--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHHHHHHHHhHHHHHH
Confidence            999999988766  445 7889999999999999999999999988776533 56788888899999999888887

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

Probab=97.46  E-value=0.004  Score=51.10  Aligned_cols=137  Identities=22%  Similarity=0.211  Sum_probs=98.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+++...+.+..+.|..+|.+..+.+.+..++....++|.-+ ..++.+.|.++|+...+. +..+...|..-|+-+.+.
T Consensus         6 ~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~-~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l~~~   83 (280)
T PF05843_consen    6 QYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFLIKL   83 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHh
Confidence            578888888899999999999997764556666656555433 346677899999988874 446788899999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCC---ChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCcccccchh
Q 025225          191 GSPADAMNIYEDMIKSPDPP---EELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYDPPE  250 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p---~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~~li  250 (256)
                      |+.+.|..+|++.... +.+   ....|...++-=.+.|+++...+  .......|+......++
T Consensus        84 ~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~~~~~~~f~  147 (280)
T PF05843_consen   84 NDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPEDNSLELFS  147 (280)
T ss_dssp             T-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTTS-HHHHHH
T ss_pred             CcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhhHHHHHH
Confidence            9999999999998876 322   23599999999999998887666  33344455544333333

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.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.40  E-value=0.0047  Score=45.30  Aligned_cols=102  Identities=8%  Similarity=-0.089  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhc
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLL  223 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~  223 (256)
                      .+..+-..+...|++++|...|+...... ..+...|..+-..+.+.|++++|...|++..+.. ..+...+..+-.++.
T Consensus        26 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~  103 (144)
T PRK15359         26 TVYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLK  103 (144)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHH
Confidence            35566778889999999999999988743 2367888899999999999999999999999763 347788888999999


Q ss_pred             CCCChHHHHHh--hhhhcCCCccccc
Q 025225          224 PHPLLRSKVKK--DFEELFPEKHAYD  247 (256)
Q Consensus       224 ~~g~~~~a~~~--~~~~~~p~~~~~~  247 (256)
                      ..|+.++|+..  ..-.+.|+...|.
T Consensus       104 ~~g~~~eAi~~~~~Al~~~p~~~~~~  129 (144)
T PRK15359        104 MMGEPGLAREAFQTAIKMSYADASWS  129 (144)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCChHHH
Confidence            99999999993  3344566654443

>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=97.37  E-value=0.0013  Score=41.23  Aligned_cols=64  Identities=17%  Similarity=0.273  Sum_probs=44.9

Q ss_pred             HHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHH
Q 025225          117 ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVI  184 (256)
Q Consensus       117 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  184 (256)
                      .+.|++++|.+.|+...+..  +-+...+-.+..+|.+.|++++|.++++++...  .|+...|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN--PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            45677888888888877774  447777777888888888888888888877763  36655555544

...

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

Probab=97.36  E-value=0.0085  Score=51.55  Aligned_cols=115  Identities=15%  Similarity=0.165  Sum_probs=94.0

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCC
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGS  192 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~  192 (256)
                      -.+...|++++|+..++.+.+.-  +-|+.-+......+.+.++.++|.+.++++...  .|+ ...+-.+=.+|.+.|+
T Consensus       314 ~~~~~~~~~d~A~~~l~~L~~~~--P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~  389 (484)
T COG4783         314 LQTYLAGQYDEALKLLQPLIAAQ--PDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGK  389 (484)
T ss_pred             HHHHHhcccchHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCC
Confidence            34556789999999999998773  556666677788999999999999999999874  576 4556677788999999


Q ss_pred             hhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          193 PADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       193 ~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +++|..++++-... .+-|+..|..|-++|...|+..++..
T Consensus       390 ~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~  429 (484)
T COG4783         390 PQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALL  429 (484)
T ss_pred             hHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHH
Confidence            99999999987755 35588899999999999987777655

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

Probab=97.34  E-value=0.0097  Score=50.61  Aligned_cols=99  Identities=20%  Similarity=0.172  Sum_probs=59.9

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCCh
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~  193 (256)
                      .....|++++|++.|++..+..  .-+...|..+-.+|.+.|++++|...+++..+.  .| +...|..+-.+|.+.|++
T Consensus        11 ~a~~~~~~~~Ai~~~~~Al~~~--P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--~P~~~~a~~~lg~~~~~lg~~   86 (356)
T PLN03088         11 EAFVDDDFALAVDLYTQAIDLD--PNNAELYADRAQANIKLGNFTEAVADANKAIEL--DPSLAKAYLRKGTACMKLEEY   86 (356)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCCH
Confidence            3445566777777777666664  445566666666666777777777777666653  23 345566666666667777


Q ss_pred             hHHHHHHHHHHhCCCCCChhHHHHHH
Q 025225          194 ADAMNIYEDMIKSPDPPEELPFRILL  219 (256)
Q Consensus       194 ~~a~~~~~~M~~~g~~p~~~t~~~li  219 (256)
                      ++|...|++..+.  .|+.......+
T Consensus        87 ~eA~~~~~~al~l--~P~~~~~~~~l  110 (356)
T PLN03088         87 QTAKAALEKGASL--APGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            7777777666654  34444443333

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.33  E-value=0.031  Score=51.66  Aligned_cols=117  Identities=12%  Similarity=0.051  Sum_probs=80.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhh-HHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQT-YTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t-~~~li~~~~~~  190 (256)
                      |-......|.+++|+.+++...+..  .-+....-.+...+.+.+++++|....++..+.  .|+..+ .+.+=.++.+.
T Consensus        92 La~i~~~~g~~~ea~~~l~~~~~~~--Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~~a~~l~~~  167 (694)
T PRK15179         92 VARALEAAHRSDEGLAVWRGIHQRF--PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILLEAKSWDEI  167 (694)
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHhhC--CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHh
Confidence            4444556778888888888777663  445566677777788888888888888877764  355544 34444455567


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |++++|.++|++....+ .-+..++..+-..+-..|+.++|..
T Consensus       168 g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~  209 (694)
T PRK15179        168 GQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARD  209 (694)
T ss_pred             cchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            88888888888877632 2236677777777777787777766

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

Probab=97.30  E-value=0.00062  Score=44.90  Aligned_cols=81  Identities=23%  Similarity=0.279  Sum_probs=49.1

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChhHHH
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPADAM  197 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~  197 (256)
                      .|+++.|+.+|+.+.+...-.|+...+-.+-.+|.+.|++++|.+++++ .+  ..|+. ...-.+-.+|.+.|++++|.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~--~~~~~~~~~~l~a~~~~~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LK--LDPSNPDIHYLLARCLLKLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HT--HHHCHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hC--CCCCCHHHHHHHHHHHHHhCCHHHHH
Confidence            4677888888888777651112344444477777888888888888877 22  11322 22223355566778888888


Q ss_pred             HHHHH
Q 025225          198 NIYED  202 (256)
Q Consensus       198 ~~~~~  202 (256)
                      ++|++
T Consensus        79 ~~l~~   83 (84)
T PF12895_consen   79 KALEK   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            77764

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.27  E-value=0.0088  Score=52.82  Aligned_cols=221  Identities=10%  Similarity=0.006  Sum_probs=140.5

Q ss_pred             cccccCCchHHHHHHHHHhcC-----CC----ccccc----cccCCCCCCCCcccCcccccccccccCCCCCCcccccc-
Q 025225            5 LFSRSKIPILASIVLQNLTKN-----PS----KNFSF----LAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKK-   70 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~-----~~----~~~ll----~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~-   70 (256)
                      .|...|+.+.|..+++.-.+.     |.    ..+++    ..+...+...++     +.+|+.+..-....   .+.. 
T Consensus       208 ~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eA-----v~ly~~AL~i~e~~---~G~~h  279 (508)
T KOG1840|consen  208 MYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEA-----VNLYEEALTIREEV---FGEDH  279 (508)
T ss_pred             HHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHH-----HHHHHHHHHHHHHh---cCCCC
Confidence            466778888888888764322     21    22222    233344555555     66666554321100   0000 


Q ss_pred             -ccchhHHHHHHHhhcCCCcHHHHHHHHHHHhh--c--cC-CCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCC--C
Q 025225           71 -LIGKEALFVILGLKRFKDDEEKLQKFIKTHVL--R--LL-KMDIV----AVLIELERQEETILAVKIFDIIRKQDW--Y  138 (256)
Q Consensus        71 -~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~--~--~~-~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~--~  138 (256)
                       -.......+-..|++.|++.+|-.-+-..+..  .  +. .|.+.    .+...++..+++++|..+++...+.-.  +
T Consensus       280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~  359 (508)
T KOG1840|consen  280 PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAP  359 (508)
T ss_pred             HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhc
Confidence             01223334455789999999986433322221  1  11 12222    267778888999999999986543310  1


Q ss_pred             CC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----C--CCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHh--
Q 025225          139 QP----DAYIYKDLIIALARTGKMNEAMQVWESMRKE----D--LFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIK--  205 (256)
Q Consensus       139 ~p----~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g--~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~--  205 (256)
                      .+    -..+|+.|=..|-..|++++|+++|++....    +  ..+. -..++.|=..|-+.+..++|.++|.+-..  
T Consensus       360 g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~  439 (508)
T KOG1840|consen  360 GEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIM  439 (508)
T ss_pred             cccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHH
Confidence            22    2478999999999999999999999987642    1  2232 45678888899999999999999987543  


Q ss_pred             --CCC--CCChhHHHHHHHHhcCCCChHHHHH
Q 025225          206 --SPD--PPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       206 --~g~--~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                        -|.  +-...||..|...|...|++++|.+
T Consensus       440 ~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~  471 (508)
T KOG1840|consen  440 KLCGPDHPDVTYTYLNLAALYRAQGNYEAAEE  471 (508)
T ss_pred             HHhCCCCCchHHHHHHHHHHHHHcccHHHHHH
Confidence              232  2234678899999999999999988

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

Probab=97.27  E-value=0.059  Score=42.23  Aligned_cols=154  Identities=14%  Similarity=0.019  Sum_probs=108.8

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      ...+.+-.+|...|+...|...+- +..+..  |+..    .+-..|-+.|+.+.|.+-|..-.+..  +-+-.+.|..=
T Consensus        36 ~arlqLal~YL~~gd~~~A~~nle-kAL~~D--Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~--p~~GdVLNNYG  110 (250)
T COG3063          36 KARLQLALGYLQQGDYAQAKKNLE-KALEHD--PSYYLAHLVRAHYYQKLGENDLADESYRKALSLA--PNNGDVLNNYG  110 (250)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHH-HHHHhC--cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC--CCccchhhhhh
Confidence            344455678999999999976554 333322  4433    35555678899999999999888775  45566777777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhC-CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCCh
Q 025225          150 IALARTGKMNEAMQVWESMRKE-DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLL  228 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~  228 (256)
                      ..+|..|++++|...|++.... ...--..||..+--+..+.|+.+.|.+.|.+-.+..- -...+.-.+.+...+.|++
T Consensus       111 ~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp-~~~~~~l~~a~~~~~~~~y  189 (250)
T COG3063         111 AFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDP-QFPPALLELARLHYKAGDY  189 (250)
T ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCc-CCChHHHHHHHHHHhcccc
Confidence            7889999999999999988875 1112246777777777789999999999998776521 1234455666777777777


Q ss_pred             HHHHH
Q 025225          229 RSKVK  233 (256)
Q Consensus       229 ~~a~~  233 (256)
                      ..|..
T Consensus       190 ~~Ar~  194 (250)
T COG3063         190 APARL  194 (250)
T ss_pred             hHHHH
Confidence            76655

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

Probab=97.24  E-value=0.017  Score=42.37  Aligned_cols=111  Identities=15%  Similarity=0.103  Sum_probs=47.3

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHH---HHHHHHhcCCHHHHHHHHHHHHhCCCCCCH--hhHHHHHHHHHHcCCh
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKD---LIIALARTGKMNEAMQVWESMRKEDLFPDS--QTYTEVIRGFLKDGSP  193 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~---li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~li~~~~~~g~~  193 (256)
                      .++...+...++.+.+..  ..++...-.   +-..+...|++++|...|+......-.|+.  ...-.|-..+...|++
T Consensus        24 ~~~~~~~~~~~~~l~~~~--~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~  101 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDY--PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQY  101 (145)
T ss_pred             CCCHHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCH
Confidence            455555555555555443  222111111   223444455555555555555554311111  1222234444455555


Q ss_pred             hHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          194 ADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       194 ~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++|+..++......+  ....+...-+.|.+.|++++|..
T Consensus       102 d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~  139 (145)
T PF09976_consen  102 DEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARA  139 (145)
T ss_pred             HHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHH
Confidence            555555544222222  22233344445555555555544

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

Probab=97.13  E-value=0.0088  Score=49.15  Aligned_cols=149  Identities=11%  Similarity=0.035  Sum_probs=107.7

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHHH-HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVA-VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      -..|.+.|-+.+|- ..++...+..--||.+. |-++|.+..+.+.|+.+|.+-.+.-  .-|+.-..-+-..+-..++.
T Consensus       230 gkCylrLgm~r~Ae-kqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f--P~~VT~l~g~ARi~eam~~~  306 (478)
T KOG1129|consen  230 GKCYLRLGMPRRAE-KQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF--PFDVTYLLGQARIHEAMEQQ  306 (478)
T ss_pred             HHHHHHhcChhhhH-HHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC--CchhhhhhhhHHHHHHHHhH
Confidence            45677778787775 55556656555577775 6678889999999999999887662  33443344556667778999


Q ss_pred             HHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          159 NEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++|.++++...+.. ..++....++-.+|.=.++++-|+.+++++.+.|+. ++..|+.+--+|.-.+.++-++-
T Consensus       307 ~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~  379 (478)
T KOG1129|consen  307 EDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLP  379 (478)
T ss_pred             HHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHH
Confidence            99999999877642 135566666777788889999999999999999985 45566666666666666665544

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

Probab=97.13  E-value=0.0086  Score=38.91  Aligned_cols=90  Identities=16%  Similarity=0.195  Sum_probs=71.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhc
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLL  223 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~  223 (256)
                      +|..+...+...|++++|...|++..+.. ..+...+..+-..+...|++++|.+.|++..+.. ..+..++..+...+.
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~   79 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYY   79 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHH
Confidence            35567778888999999999999987742 1234677888888889999999999999987764 223467888888999


Q ss_pred             CCCChHHHHHhh
Q 025225          224 PHPLLRSKVKKD  235 (256)
Q Consensus       224 ~~g~~~~a~~~~  235 (256)
                      ..|++++|....
T Consensus        80 ~~~~~~~a~~~~   91 (100)
T cd00189          80 KLGKYEEALEAY   91 (100)
T ss_pred             HHHhHHHHHHHH
Confidence            999999888743

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

Probab=97.13  E-value=0.031  Score=44.69  Aligned_cols=155  Identities=14%  Similarity=0.114  Sum_probs=110.1

Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHH-HH--HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIV-AV--LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAM  162 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~-~l--i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~  162 (256)
                      .++.++.+..+.+.+.......+.. .+  ...|++.+++++|++....    + -.......|  +..+.+..++|-|+
T Consensus        85 e~~~~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~----~-~~lE~~Al~--VqI~lk~~r~d~A~  157 (299)
T KOG3081|consen   85 ESNKKSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHL----G-ENLEAAALN--VQILLKMHRFDLAE  157 (299)
T ss_pred             cchhHHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhc----c-chHHHHHHH--HHHHHHHHHHHHHH
Confidence            5555666666666666555555533 23  3457889999999988876    2 133333333  45567888899999


Q ss_pred             HHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhhhh
Q 025225          163 QVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEE  238 (256)
Q Consensus       163 ~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~  238 (256)
                      +.+++|.+-   -+..|.+.|-.+|.+    .+++.+|+-+|++|-+. ..|++-+-+....++...|++++|-.....-
T Consensus       158 ~~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~ea  233 (299)
T KOG3081|consen  158 KELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEA  233 (299)
T ss_pred             HHHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHH
Confidence            999999984   467788878777776    45789999999999764 6789999999999999999999997744444


Q ss_pred             cCCCcccccchhH
Q 025225          239 LFPEKHAYDPPEE  251 (256)
Q Consensus       239 ~~p~~~~~~~li~  251 (256)
                      +..|.--+.+|++
T Consensus       234 L~kd~~dpetL~N  246 (299)
T KOG3081|consen  234 LDKDAKDPETLAN  246 (299)
T ss_pred             HhccCCCHHHHHH
Confidence            4444333444443

>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=97.08  E-value=0.004  Score=45.66  Aligned_cols=70  Identities=23%  Similarity=0.311  Sum_probs=34.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH-----hCCCCCChhHH
Q 025225          145 YKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI-----KSPDPPEELPF  215 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~-----~~g~~p~~~t~  215 (256)
                      ...++..+...|++++|.++.+.+.... +-|...|-.+|.+|...|+...|.++|+++.     +.|+.|+..|-
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            3444455555666666666666655521 1245566666666666666666666665553     23666665553

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

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

Probab=97.07  E-value=0.015  Score=49.87  Aligned_cols=205  Identities=9%  Similarity=-0.011  Sum_probs=141.2

Q ss_pred             CchHHHHHHHHHhcCCC-----ccccccccCC-CCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhh
Q 025225           11 IPILASIVLQNLTKNPS-----KNFSFLAFKP-KSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLK   84 (256)
Q Consensus        11 ~~~~A~~l~~~m~~~~~-----~~~ll~a~~~-~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~   84 (256)
                      +.+++.+-.+.+...|+     +.+.+.+++- ..+++.+     +++|+++.+..+    .+.+.+  ..+..++  |.
T Consensus       242 q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a-----~s~Feei~knDP----YRl~dm--dlySN~L--Yv  308 (559)
T KOG1155|consen  242 QHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQA-----ESVFEEIRKNDP----YRLDDM--DLYSNVL--YV  308 (559)
T ss_pred             HHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHH-----HHHHHHHHhcCC----CcchhH--HHHhHHH--HH
Confidence            44555555555555555     2333333332 3457778     999988887633    222222  1111111  23


Q ss_pred             cCCCcHHHHHHHHHHHhhccCCCcHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 025225           85 RFKDDEEKLQKFIKTHVLRLLKMDIVAVL-IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQ  163 (256)
Q Consensus        85 ~~~~~~~a~~~~~~~~~~~~~~~~~~~li-~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~  163 (256)
                      +..+.+-+. ....-......+|..-.+| +=|+-.++.++|...|+...+.+  +-....|+.+=.-|....+...|.+
T Consensus       309 ~~~~skLs~-LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN--p~~~~aWTLmGHEyvEmKNt~AAi~  385 (559)
T KOG1155|consen  309 KNDKSKLSY-LAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN--PKYLSAWTLMGHEYVEMKNTHAAIE  385 (559)
T ss_pred             HhhhHHHHH-HHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC--cchhHHHHHhhHHHHHhcccHHHHH
Confidence            333222221 1112233455667655544 44555788999999999999887  6778899999999999999999999


Q ss_pred             HHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          164 VWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       164 ~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      -+....+-+ +.|-..|=.|=.+|.-.+.+.-|+-.|++-.+-. +-|+..|.+|=++|.+.++.++|++
T Consensus       386 sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiK  453 (559)
T KOG1155|consen  386 SYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIK  453 (559)
T ss_pred             HHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHH
Confidence            999988732 3488999999999999999999999999876541 2378999999999999999999998

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

Probab=97.04  E-value=0.14  Score=43.14  Aligned_cols=155  Identities=12%  Similarity=0.005  Sum_probs=96.5

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHH---HHHH----cCCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHHH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLI---ELER----QEETILAVKIFDIIRKQDWYQPD-AYIYKDLIIALA  153 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~---~~~~----~~~~~~a~~~~~~m~~~~~~~p~-~~~y~~li~~~~  153 (256)
                      .+...|+.+++...+ +.....  .|+....+.   .+..    .+....+.+.+..  ..+ ..|+ ......+-..+.
T Consensus        52 ~~~~~g~~~~A~~~~-~~~l~~--~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~--~~~-~~~~~~~~~~~~a~~~~  125 (355)
T cd05804          52 SAWIAGDLPKALALL-EQLLDD--YPRDLLALKLHLGAFGLGDFSGMRDHVARVLPL--WAP-ENPDYWYLLGMLAFGLE  125 (355)
T ss_pred             HHHHcCCHHHHHHHH-HHHHHH--CCCcHHHHHHhHHHHHhcccccCchhHHHHHhc--cCc-CCCCcHHHHHHHHHHHH
Confidence            445678888887433 444332  243321111   2222    3445555555554  112 2333 334445566778


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC-CCCh--hHHHHHHHHhcCCCChHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD-PPEE--LPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~-~p~~--~t~~~li~~~~~~g~~~~  230 (256)
                      ..|++++|.+.+++..+.. +.+...+..+-..|...|++++|.+++++.....- .|+.  ..|-.+...+...|++++
T Consensus       126 ~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~  204 (355)
T cd05804         126 EAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEA  204 (355)
T ss_pred             HcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHH
Confidence            8899999999999988753 22356677777888889999999999998776522 2332  345578888999999999


Q ss_pred             HHHhhhhhcCCCc
Q 025225          231 KVKKDFEELFPEK  243 (256)
Q Consensus       231 a~~~~~~~~~p~~  243 (256)
                      |......-+.+++
T Consensus       205 A~~~~~~~~~~~~  217 (355)
T cd05804         205 ALAIYDTHIAPSA  217 (355)
T ss_pred             HHHHHHHHhcccc
Confidence            9986555454443

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.

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

Probab=97.00  E-value=0.06  Score=39.37  Aligned_cols=120  Identities=13%  Similarity=0.070  Sum_probs=80.7

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH--HHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV------AVLIELERQEETILAVKIFDIIRKQDWYQPDA--YIYKDL  148 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~--~~y~~l  148 (256)
                      ..++..+ ..++..++. ..++.+....- .+..      .+=..+...|++++|...|++..... ..|+.  ...-.+
T Consensus        16 ~~~~~~~-~~~~~~~~~-~~~~~l~~~~~-~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~-~d~~l~~~a~l~L   91 (145)
T PF09976_consen   16 EQALQAL-QAGDPAKAE-AAAEQLAKDYP-SSPYAALAALQLAKAAYEQGDYDEAKAALEKALANA-PDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHH-HCCCHHHHH-HHHHHHHHHCC-CChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-CCHHHHHHHHHHH
Confidence            3344444 466676664 43444444321 1212      24567788999999999999999875 23332  234446


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHH
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYED  202 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  202 (256)
                      -..+...|++++|...++.......  ....+...=..|.+.|+.++|...|+.
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            6778889999999999987544332  334556677778999999999999975

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

Probab=96.99  E-value=0.025  Score=52.09  Aligned_cols=171  Identities=11%  Similarity=0.060  Sum_probs=115.8

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      +.-|-+.|+...|++.+.+...-.+ ..|..       .++..|...++-+.|.+.++.-...+.-..+...+|+++..|
T Consensus       248 s~L~~~~G~~~~Am~~f~~l~~~~p-~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~  326 (895)
T KOG2076|consen  248 SSLYQKTGDLKRAMETFLQLLQLDP-PVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELF  326 (895)
T ss_pred             HHHHHHhChHHHHHHHHHHHHhhCC-chhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHH
Confidence            4566778888888876654433222 12222       257777777878888888887766332356667788888888


Q ss_pred             HhcCCHHHHHHHHHHHHhCCC---------------------------C-------------------------------
Q 025225          153 ARTGKMNEAMQVWESMRKEDL---------------------------F-------------------------------  174 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~---------------------------~-------------------------------  174 (256)
                      .+...++.|......+.....                           .                               
T Consensus       327 l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~  406 (895)
T KOG2076|consen  327 LKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVED  406 (895)
T ss_pred             HHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHh
Confidence            888777777777766655111                           1                               


Q ss_pred             -----CCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhhhhcCCCcccccch
Q 025225          175 -----PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPP  249 (256)
Q Consensus       175 -----p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~p~~~~~~~l  249 (256)
                           -+...|.-+-.+|.+.|++..|+.+|..+......-+...|--+-++|-..|..++|++--.+-+.-++.++++.
T Consensus       407 n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~R  486 (895)
T KOG2076|consen  407 NVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDAR  486 (895)
T ss_pred             cCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhh
Confidence                 122335566777888999999999999998875555677888899999999999999883333334444555554


Q ss_pred             hH
Q 025225          250 EE  251 (256)
Q Consensus       250 i~  251 (256)
                      |.
T Consensus       487 i~  488 (895)
T KOG2076|consen  487 IT  488 (895)
T ss_pred             hh
Confidence            43

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=96.99  E-value=0.095  Score=48.52  Aligned_cols=120  Identities=13%  Similarity=0.114  Sum_probs=97.6

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      -....+.|+.++|.. +++...  .+.||..    .+...+.+.+++++|+..+++.....  .-+....+.+-.++...
T Consensus        93 a~i~~~~g~~~ea~~-~l~~~~--~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~--p~~~~~~~~~a~~l~~~  167 (694)
T PRK15179         93 ARALEAAHRSDEGLA-VWRGIH--QRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG--SSSAREILLEAKSWDEI  167 (694)
T ss_pred             HHHHHHcCCcHHHHH-HHHHHH--hhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHh
Confidence            345567899999874 444432  3567766    48889999999999999999999886  55667778888889999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          156 GKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      |++++|.++|++....  .|+ ..++..+=..+-+.|+.++|...|++-.+.
T Consensus       168 g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        168 GQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             cchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            9999999999999972  344 788888888899999999999999998765

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

Probab=96.98  E-value=0.069  Score=45.12  Aligned_cols=91  Identities=19%  Similarity=0.178  Sum_probs=74.4

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCCH--hhHHHHHHHHHHc
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDL-FPDS--QTYTEVIRGFLKD  190 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~--~t~~~li~~~~~~  190 (256)
                      ..+...|++++|.+.+++..+..  +.+...+..+-..|...|++++|...+++.....- .|+.  ..|-.+-..+...
T Consensus       122 ~~~~~~G~~~~A~~~~~~al~~~--p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~  199 (355)
T cd05804         122 FGLEEAGQYDRAEEAARRALELN--PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLER  199 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHC
Confidence            46678999999999999999886  56677888888999999999999999998876421 2333  3455788889999


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |+.++|.+++++....
T Consensus       200 G~~~~A~~~~~~~~~~  215 (355)
T cd05804         200 GDYEAALAIYDTHIAP  215 (355)
T ss_pred             CCHHHHHHHHHHHhcc
Confidence            9999999999998654

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.

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.98  E-value=0.019  Score=47.90  Aligned_cols=102  Identities=18%  Similarity=0.159  Sum_probs=86.3

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .-|.-+...|+.+.|.++-.+.+     .||-.-|-..|.+|+..+++++-+++-.+ +     -..+-|-..+..|.+.
T Consensus       182 ~Ti~~li~~~~~k~A~kl~k~Fk-----v~dkrfw~lki~aLa~~~~w~eL~~fa~s-k-----KsPIGyepFv~~~~~~  250 (319)
T PF04840_consen  182 DTIRKLIEMGQEKQAEKLKKEFK-----VPDKRFWWLKIKALAENKDWDELEKFAKS-K-----KSPIGYEPFVEACLKY  250 (319)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHcC-----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC-C-----CCCCChHHHHHHHHHC
Confidence            45777788899999988877765     69999999999999999999999887543 2     2458999999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |+..+|..+..+          .++.--+..|.+.|++.+|.+
T Consensus       251 ~~~~eA~~yI~k----------~~~~~rv~~y~~~~~~~~A~~  283 (319)
T PF04840_consen  251 GNKKEASKYIPK----------IPDEERVEMYLKCGDYKEAAQ  283 (319)
T ss_pred             CCHHHHHHHHHh----------CChHHHHHHHHHCCCHHHHHH
Confidence            999999999887          334677889999999999987

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

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=96.97  E-value=0.065  Score=47.48  Aligned_cols=159  Identities=13%  Similarity=0.053  Sum_probs=110.5

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhh-----ccCC-CcHHHHHH----HHHHcCCHHHHHHHHHHHHhc-----CCCC
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVL-----RLLK-MDIVAVLI----ELERQEETILAVKIFDIIRKQ-----DWYQ  139 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~-----~~~~-~~~~~li~----~~~~~~~~~~a~~~~~~m~~~-----~~~~  139 (256)
                      ....+...|...|++++|...+ +....     .|.. |.+.++++    .|...+.+.+|..+|+++...     |...
T Consensus       201 ~~~~La~~y~~~g~~e~A~~l~-k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  201 TLRNLAEMYAVQGRLEKAEPLC-KQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHhccHHHHHHHH-HHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            3344678899999999997444 33322     2322 34444444    566789999999999987633     2112


Q ss_pred             CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh---C--C-CCCCHh-hHHHHHHHHHHcCChhHHHHHHHHHHhC---CC
Q 025225          140 PD-AYIYKDLIIALARTGKMNEAMQVWESMRK---E--D-LFPDSQ-TYTEVIRGFLKDGSPADAMNIYEDMIKS---PD  208 (256)
Q Consensus       140 p~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~---~--g-~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~M~~~---g~  208 (256)
                      |. ..+++.|-.+|++.|++++|...+++..+   .  | ..|.+. -++.+...|+..+++++|..++.+-.+.   -.
T Consensus       280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~  359 (508)
T KOG1840|consen  280 PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAP  359 (508)
T ss_pred             HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhc
Confidence            22 35677777789999999999988886653   1  2 223443 3667778888999999999999876532   12


Q ss_pred             CCC----hhHHHHHHHHhcCCCChHHHHHh
Q 025225          209 PPE----ELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       209 ~p~----~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      .++    ..+++.|-..|.+.|++.+|.++
T Consensus       360 g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~  389 (508)
T KOG1840|consen  360 GEDNVNLAKIYANLAELYLKMGKYKEAEEL  389 (508)
T ss_pred             cccchHHHHHHHHHHHHHHHhcchhHHHHH
Confidence            233    36789999999999999999883

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

Probab=96.95  E-value=0.07  Score=46.96  Aligned_cols=167  Identities=13%  Similarity=0.101  Sum_probs=91.6

Q ss_pred             chhHHHHHHHhhcCCCcHHHHHHHHHHHhh-cc-CCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 025225           73 GKEALFVILGLKRFKDDEEKLQKFIKTHVL-RL-LKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLII  150 (256)
Q Consensus        73 ~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~-~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~  150 (256)
                      +..|+..-+.|+-.+..++|+..+....+- .| ..|..+ +=--|.+.++++.|.+.|.+.....  +-|+...+-+=-
T Consensus       346 gpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LY-lgmey~~t~n~kLAe~Ff~~A~ai~--P~Dplv~~Elgv  422 (611)
T KOG1173|consen  346 GPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLY-LGMEYMRTNNLKLAEKFFKQALAIA--PSDPLVLHELGV  422 (611)
T ss_pred             cHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHH-HHHHHHHhccHHHHHHHHHHHHhcC--CCcchhhhhhhh
Confidence            457777777788888888877555432211 12 122222 1223455666777777777666553  455555555544


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC--CCC----CCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC
Q 025225          151 ALARTGKMNEAMQVWESMRKE--DLF----PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP  224 (256)
Q Consensus       151 ~~~~~g~~~~a~~~~~~m~~~--g~~----p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~  224 (256)
                      ..-..+.+.+|...|+.-+..  .+.    .-..+++.|=..|.+.++.++|+..|++-... .+-|..||.++--.|..
T Consensus       423 vay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-~~k~~~~~asig~iy~l  501 (611)
T KOG1173|consen  423 VAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-SPKDASTHASIGYIYHL  501 (611)
T ss_pred             eeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-CCCchhHHHHHHHHHHH
Confidence            444556666666666655421  111    12344555556666666666666666655433 12355666666666666


Q ss_pred             CCChHHHHH--hhhhhcCCCc
Q 025225          225 HPLLRSKVK--KDFEELFPEK  243 (256)
Q Consensus       225 ~g~~~~a~~--~~~~~~~p~~  243 (256)
                      .|.++.|++  -+.-.+.||.
T Consensus       502 lgnld~Aid~fhKaL~l~p~n  522 (611)
T KOG1173|consen  502 LGNLDKAIDHFHKALALKPDN  522 (611)
T ss_pred             hcChHHHHHHHHHHHhcCCcc
Confidence            666666666  3333444544

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

Probab=96.94  E-value=0.02  Score=49.49  Aligned_cols=144  Identities=14%  Similarity=0.129  Sum_probs=101.9

Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHH-HHHHHH---HHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIV-AVLIEL---ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEA  161 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~---~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a  161 (256)
                      .+++++|+..|-+ .  ..+.|... +.|.-|   .+.+.++++...|++.++.  ++--+..||-.-..+...+++++|
T Consensus       407 L~q~e~A~aDF~K-a--i~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~A  481 (606)
T KOG0547|consen  407 LQQYEEAIADFQK-A--ISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDKA  481 (606)
T ss_pred             HHHHHHHHHHHHH-H--hhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHHH
Confidence            4556777755532 2  23445433 444443   3678999999999999988  577788999999999999999999


Q ss_pred             HHHHHHHHhCC-----CCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          162 MQVWESMRKED-----LFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       162 ~~~~~~m~~~g-----~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      .+.|+...+..     +..+  ...--+++-.= ..+++..|.+++++-.+..-+ ....|.+|-.--.+.|++++|+++
T Consensus       482 ~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAiel  559 (606)
T KOG0547|consen  482 VKQYDKAIELEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIEL  559 (606)
T ss_pred             HHHHHHHHhhccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHH
Confidence            99999887631     1111  12222222222 358999999999988766322 457888999999999999999995


Q ss_pred             hh
Q 025225          235 DF  236 (256)
Q Consensus       235 ~~  236 (256)
                      +.
T Consensus       560 FE  561 (606)
T KOG0547|consen  560 FE  561 (606)
T ss_pred             HH
Confidence            44

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

Probab=96.90  E-value=0.012  Score=54.68  Aligned_cols=111  Identities=15%  Similarity=0.280  Sum_probs=93.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHH
Q 025225          120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNI  199 (256)
Q Consensus       120 ~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  199 (256)
                      +..++|+++|.+..+..  +.|...-|-+=..++.+|++++|..+|.+..+... -+..+|-.+-..|...|++..|+++
T Consensus       626 k~~~KAlq~y~kvL~~d--pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqm  702 (1018)
T KOG2002|consen  626 KHQEKALQLYGKVLRND--PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQM  702 (1018)
T ss_pred             HHHHHHHHHHHHHHhcC--cchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHH
Confidence            45689999999988886  67888888888889999999999999999888643 2446788888999999999999999


Q ss_pred             HHHHH-hCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          200 YEDMI-KSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       200 ~~~M~-~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |+.-. ...-.-++...+.|-+++.+.|.+.++++
T Consensus       703 Ye~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~  737 (1018)
T KOG2002|consen  703 YENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKE  737 (1018)
T ss_pred             HHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHH
Confidence            98654 44556678888899999999999999988

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=96.90  E-value=0.0073  Score=44.24  Aligned_cols=67  Identities=25%  Similarity=0.322  Sum_probs=52.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHhh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK-----EDLFPDSQT  179 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t  179 (256)
                      .++..+...|++++|.++...+....  +.|...|-.+|.+|...|+..+|.++|+++.+     .|+.|+..|
T Consensus        67 ~l~~~~~~~~~~~~a~~~~~~~l~~d--P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   67 RLAEALLEAGDYEEALRLLQRALALD--PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHHS--TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHhccCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            36677788999999999999999986  77899999999999999999999999998864     389898765

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

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.87  E-value=0.13  Score=40.74  Aligned_cols=128  Identities=13%  Similarity=0.060  Sum_probs=88.2

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhh-ccCCCcHH-H---HHHHHHHc--------CCHHHHHHHHHHHHhcCCCCCCH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVL-RLLKMDIV-A---VLIELERQ--------EETILAVKIFDIIRKQDWYQPDA  142 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~-~---li~~~~~~--------~~~~~a~~~~~~m~~~~~~~p~~  142 (256)
                      +..+-..+-+.++.++|+..+ +...+ ..-.|... +   +-.++.+.        |+.++|.+.|+...+..  +-+.
T Consensus        73 ~~~la~~~~~~~~~~~A~~~~-~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--p~~~  149 (235)
T TIGR03302        73 QLDLAYAYYKSGDYAEAIAAA-DRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY--PNSE  149 (235)
T ss_pred             HHHHHHHHHhcCCHHHHHHHH-HHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC--CCCh
Confidence            344567788899999998655 44433 33233321 1   22223322        77999999999998775  2222


Q ss_pred             HHHH-----------------HHHHHHHhcCCHHHHHHHHHHHHhCC--CCCCHhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          143 YIYK-----------------DLIIALARTGKMNEAMQVWESMRKED--LFPDSQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       143 ~~y~-----------------~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      ..+.                 .+-..|.+.|++++|...|++..+..  -......+..+...+.+.|+.++|..+++.+
T Consensus       150 ~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l  229 (235)
T TIGR03302       150 YAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVL  229 (235)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            2222                 23455778899999999999988742  1223578899999999999999999999988


Q ss_pred             HhC
Q 025225          204 IKS  206 (256)
Q Consensus       204 ~~~  206 (256)
                      ...
T Consensus       230 ~~~  232 (235)
T TIGR03302       230 GAN  232 (235)
T ss_pred             Hhh
Confidence            765

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).

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.87  E-value=0.032  Score=38.70  Aligned_cols=88  Identities=17%  Similarity=0.194  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC--CCChhHHHH
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPD----SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD--PPEELPFRI  217 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~--~p~~~t~~~  217 (256)
                      ++-.+...+.+.|++++|.+.|+++.+..  |+    ...+..+...+.+.|++++|...|++.....-  ......+..
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~   81 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKY--PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLK   81 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHH
Confidence            56667778889999999999999998742  33    34566788899999999999999999886521  223456778


Q ss_pred             HHHHhcCCCChHHHHH
Q 025225          218 LLKGLLPHPLLRSKVK  233 (256)
Q Consensus       218 li~~~~~~g~~~~a~~  233 (256)
                      +...+.+.|+.++|.+
T Consensus        82 ~~~~~~~~~~~~~A~~   97 (119)
T TIGR02795        82 LGMSLQELGDKEKAKA   97 (119)
T ss_pred             HHHHHHHhCChHHHHH
Confidence            8888999999999988

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.

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

Probab=96.82  E-value=0.058  Score=48.18  Aligned_cols=187  Identities=11%  Similarity=0.033  Sum_probs=126.7

Q ss_pred             cccccCCchHHHHHHHHHhcCCC---ccccccccCC--CCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS---KNFSFLAFKP--KSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~---~~~ll~a~~~--~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .|+=.++.+.|++.|+...+-+-   |.-.+.+.-.  ....+.+     ...|+......++.    +|     .|.-+
T Consensus       430 cfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a-----~~~fr~Al~~~~rh----Yn-----AwYGl  495 (638)
T KOG1126|consen  430 CFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKA-----MKSFRKALGVDPRH----YN-----AWYGL  495 (638)
T ss_pred             hhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhH-----HHHHHhhhcCCchh----hH-----HHHhh
Confidence            35667888999999998765443   5555433321  2233344     56664433332222    22     23333


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      -..|.|.++.+.|. ..++..  ..+.|...    .+-..+-+.|+.++|++++++.....  ..|+..-=-....+...
T Consensus       496 G~vy~Kqek~e~Ae-~~fqkA--~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld--~kn~l~~~~~~~il~~~  570 (638)
T KOG1126|consen  496 GTVYLKQEKLEFAE-FHFQKA--VEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLD--PKNPLCKYHRASILFSL  570 (638)
T ss_pred             hhheeccchhhHHH-HHHHhh--hcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcC--CCCchhHHHHHHHHHhh
Confidence            45678999999985 444433  33445443    25566678899999999999998886  45655555566777788


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCCh
Q 025225          156 GKMNEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEE  212 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~  212 (256)
                      ++.++|...++++++  +.|+. ..|-.+-..|-+.|+.+.|+.-|.-+.+..-+++.
T Consensus       571 ~~~~eal~~LEeLk~--~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  571 GRYVEALQELEELKE--LVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             cchHHHHHHHHHHHH--hCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            999999999999998  45764 66777788899999999999999888877555544

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=96.78  E-value=0.17  Score=44.50  Aligned_cols=125  Identities=18%  Similarity=0.198  Sum_probs=102.5

Q ss_pred             cCCCcHH--HHHHHHHHcCCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHH-HHHhCCCCCCHhh
Q 025225          104 LLKMDIV--AVLIELERQEETILAVKIFDIIRKQDWYQP-DAYIYKDLIIALARTGKMNEAMQVWE-SMRKEDLFPDSQT  179 (256)
Q Consensus       104 ~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~y~~li~~~~~~g~~~~a~~~~~-~m~~~g~~p~~~t  179 (256)
                      ...|+..  .+|+.-.+..-++.|..+|.+..+.+ ..+ .++.++++|.-||. ++.+-|.++|+ -|++.   +|...
T Consensus       362 ~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~-r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf---~d~p~  436 (656)
T KOG1914|consen  362 DIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDK-RTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKF---GDSPE  436 (656)
T ss_pred             ccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhcc-CCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhc---CCChH
Confidence            3445544  58888889889999999999999998 555 99999999998874 67889999999 56664   45544


Q ss_pred             H-HHHHHHHHHcCChhHHHHHHHHHHhCCCCCC--hhHHHHHHHHhcCCCChHHHHH
Q 025225          180 Y-TEVIRGFLKDGSPADAMNIYEDMIKSPDPPE--ELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       180 ~-~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      | ...++-+...++=..+..+|++....++.|+  ...|..+|+-=..-|++...++
T Consensus       437 yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~  493 (656)
T KOG1914|consen  437 YVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILK  493 (656)
T ss_pred             HHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHH
Confidence            4 5677888888999999999999998866655  4789999999999999998877

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.78  E-value=0.0061  Score=38.10  Aligned_cols=63  Identities=22%  Similarity=0.449  Sum_probs=49.4

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILL  219 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li  219 (256)
                      ...|++++|.++|++..+.  .| |...+-.+...|.+.|++++|.+++++....  .|+...|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            4678999999999998774  24 6677778999999999999999999998877  45655555544

...

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.77  E-value=0.1  Score=39.39  Aligned_cols=109  Identities=15%  Similarity=0.174  Sum_probs=72.9

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPD--AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFL  188 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~  188 (256)
                      +-..+...|++++|...|++..+.. ..+.  ...|..+-..|.+.|++++|...+++..+.  .| +...+..+-..|.
T Consensus        41 lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~  117 (172)
T PRK02603         41 DGMSAQADGEYAEALENYEEALKLE-EDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIAVIYH  117 (172)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHh-hccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHH
Confidence            5556677899999999999888664 2222  467888889999999999999999988774  34 3455666666666


Q ss_pred             HcCC--------------hhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCC
Q 025225          189 KDGS--------------PADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPL  227 (256)
Q Consensus       189 ~~g~--------------~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~  227 (256)
                      ..|+              +++|.+++.+....    ++..|..++.-+...|+
T Consensus       118 ~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~----~p~~~~~~~~~~~~~~~  166 (172)
T PRK02603        118 KRGEKAEEAGDQDEAEALFDKAAEYWKQAIRL----APNNYIEAQNWLKTTGR  166 (172)
T ss_pred             HcCChHhHhhCHHHHHHHHHHHHHHHHHHHhh----CchhHHHHHHHHHhcCc
Confidence            6665              34455555554443    33335555555554443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.75  E-value=0.11  Score=36.73  Aligned_cols=101  Identities=17%  Similarity=0.130  Sum_probs=66.9

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH-----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC----HHHHHHHHHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-----AVLIELERQEETILAVKIFDIIRKQDWYQPD----AYIYKDLIIA  151 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~~li~~  151 (256)
                      ..+-..|+.++|+ .+++.....|+.....     .+=+.+...|++++|..++++.....   |+    ......+-.+
T Consensus         9 ~a~d~~G~~~~Ai-~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~---p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen    9 WAHDSLGREEEAI-PLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF---PDDELNAALRVFLALA   84 (120)
T ss_pred             HHHHhcCCHHHHH-HHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC---CCccccHHHHHHHHHH
Confidence            3456678888887 4556666677655433     25566777888888888888877653   33    1222223346


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK  189 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  189 (256)
                      +...|+.++|.+.+-....    ++...|.--|..|+.
T Consensus        85 L~~~gr~~eAl~~~l~~la----~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   85 LYNLGRPKEALEWLLEALA----ETLPRYRRAIRFYAD  118 (120)
T ss_pred             HHHCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHHh
Confidence            6677888888888877665    566677777777754

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

Probab=96.67  E-value=0.018  Score=46.49  Aligned_cols=34  Identities=12%  Similarity=0.269  Sum_probs=22.7

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225          120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus       120 ~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      +.++-....+..|++-| +.-|..+|+.||+.+-+
T Consensus        86 ~HveFIy~ALk~m~eyG-VerDl~vYk~LlnvfPK  119 (406)
T KOG3941|consen   86 THVEFIYTALKYMKEYG-VERDLDVYKGLLNVFPK  119 (406)
T ss_pred             chHHHHHHHHHHHHHhc-chhhHHHHHHHHHhCcc
Confidence            45666666666777777 77777777777766543

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

Probab=96.66  E-value=0.013  Score=36.31  Aligned_cols=55  Identities=24%  Similarity=0.223  Sum_probs=33.4

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      ..+.+.|++++|.+.|++..+..  .-+...+-.+-.++...|++++|...|++..+
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34556666666666666666654  33555666666666666666666666666654

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

Probab=96.64  E-value=0.11  Score=45.04  Aligned_cols=116  Identities=16%  Similarity=0.113  Sum_probs=79.2

Q ss_pred             hhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHHHhcCC
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPD-AYIYKDLIIALARTGK  157 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~y~~li~~~~~~g~  157 (256)
                      +-..+..++|...+ +...+  -.|+..    .....+.+.++.++|.+.++.+....   |+ ....-.+-.+|.+.|+
T Consensus       316 ~~~~~~~d~A~~~l-~~L~~--~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~---P~~~~l~~~~a~all~~g~  389 (484)
T COG4783         316 TYLAGQYDEALKLL-QPLIA--AQPDNPYYLELAGDILLEANKAKEAIERLKKALALD---PNSPLLQLNLAQALLKGGK  389 (484)
T ss_pred             HHHhcccchHHHHH-HHHHH--hCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC---CCccHHHHHHHHHHHhcCC
Confidence            34566677776433 33322  224333    46677778888888888888887663   44 5666667778888888


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      +.+|..+++..... .+-|...|..|-.+|...|+..++..-..++..
T Consensus       390 ~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~~  436 (484)
T COG4783         390 PQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARAEGYA  436 (484)
T ss_pred             hHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHHHHHH
Confidence            88888888876654 334778888888888888877777766666554

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

Probab=96.64  E-value=0.0015  Score=43.02  Aligned_cols=78  Identities=17%  Similarity=0.281  Sum_probs=56.6

Q ss_pred             cCCHHHHHHHHHHHHhCCC-CCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          155 TGKMNEAMQVWESMRKEDL-FPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .|+++.|..+|+++.+..- .|+...+-.+-.+|.+.|++++|.+++++ .+.+.. +....-.+-++|.+.|++++|++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~-~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPS-NPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHC-HHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCC-CHHHHHHHHHHHHHhCCHHHHHH
Confidence            5789999999999998532 22445555588999999999999999998 322221 22344456788999999999988


Q ss_pred             h
Q 025225          234 K  234 (256)
Q Consensus       234 ~  234 (256)
                      .
T Consensus        80 ~   80 (84)
T PF12895_consen   80 A   80 (84)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=96.62  E-value=0.12  Score=47.86  Aligned_cols=176  Identities=13%  Similarity=0.034  Sum_probs=117.3

Q ss_pred             CCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC----cHHHHHH
Q 025225           39 SPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM----DIVAVLI  114 (256)
Q Consensus        39 ~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~li~  114 (256)
                      |+.+.+     ..++.+..+..++.         ...|..+-..|-+.|+.++++..+   +...-+.|    .+..+=.
T Consensus       153 g~~eeA-----~~i~~EvIkqdp~~---------~~ay~tL~~IyEqrGd~eK~l~~~---llAAHL~p~d~e~W~~lad  215 (895)
T KOG2076|consen  153 GDLEEA-----EEILMEVIKQDPRN---------PIAYYTLGEIYEQRGDIEKALNFW---LLAAHLNPKDYELWKRLAD  215 (895)
T ss_pred             CCHHHH-----HHHHHHHHHhCccc---------hhhHHHHHHHHHHcccHHHHHHHH---HHHHhcCCCChHHHHHHHH
Confidence            555555     66666666555544         456666666777888888876422   22233333    2334555


Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHH----HHHHHHc
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEV----IRGFLKD  190 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l----i~~~~~~  190 (256)
                      -..+.|++++|.-.|.+..+..  +++...+---...|-+.|+...|.+-|.++....-..|..-+-.+    +..|-..
T Consensus       216 ls~~~~~i~qA~~cy~rAI~~~--p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~  293 (895)
T KOG2076|consen  216 LSEQLGNINQARYCYSRAIQAN--PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITH  293 (895)
T ss_pred             HHHhcccHHHHHHHHHHHHhcC--CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHh
Confidence            5667788889988888888876  566666666677888889999999888888875322222223333    4445556


Q ss_pred             CChhHHHHHHHHHHh-CCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          191 GSPADAMNIYEDMIK-SPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       191 g~~~~a~~~~~~M~~-~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++.+.|.+.++.-.. .+-..+...+++++..|.+...++.+..
T Consensus       294 ~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~  337 (895)
T KOG2076|consen  294 NERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALM  337 (895)
T ss_pred             hHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhH
Confidence            777888888876654 3445677788888888888888888777

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.58  E-value=0.035  Score=39.28  Aligned_cols=54  Identities=13%  Similarity=0.132  Sum_probs=28.4

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPD--AYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      +-..|+.++|+.+|.+-...| ...+  ...+=.+-++|...|++++|..+|++...
T Consensus        11 ~d~~G~~~~Ai~~Y~~Al~~g-L~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen   11 HDSLGREEEAIPLYRRALAAG-LSGADRRRALIQLASTLRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHhcCCHHHHHHHHHHHHHcC-CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            334566666666666666555 3222  12333344455555666666666665554

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.58  E-value=0.075  Score=43.93  Aligned_cols=129  Identities=15%  Similarity=0.203  Sum_probs=91.3

Q ss_pred             CcHHHHHH---HHHHHhhccCCCcHHHHHHHHHHcC---------CHHHHHHHHHHHHhcCCC--CCCHHHHHHHHHHHH
Q 025225           88 DDEEKLQK---FIKTHVLRLLKMDIVAVLIELERQE---------ETILAVKIFDIIRKQDWY--QPDAYIYKDLIIALA  153 (256)
Q Consensus        88 ~~~~a~~~---~~~~~~~~~~~~~~~~li~~~~~~~---------~~~~a~~~~~~m~~~~~~--~p~~~~y~~li~~~~  153 (256)
                      +++++++.   +++.+.+.|.+-+.++.+.++.-..         ....|..+|+.|++..++  .++..++.+|+..  
T Consensus        73 ~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--  150 (297)
T PF13170_consen   73 DPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--  150 (297)
T ss_pred             CHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--
Confidence            47776654   4567788888888786666554322         368999999999998743  5777888888776  


Q ss_pred             hcCC----HHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCC---hhHHHHHHHHHHhCCCCCChhHHHHH
Q 025225          154 RTGK----MNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGS---PADAMNIYEDMIKSPDPPEELPFRIL  218 (256)
Q Consensus       154 ~~g~----~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~---~~~a~~~~~~M~~~g~~p~~~t~~~l  218 (256)
                      ..++    .+.++.+|+.+.+.|+..+ ..-+-+-|-+++....   +.++.++++.+.+.|+++....|..+
T Consensus       151 ~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  151 TSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             ccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence            3333    5777889999998887764 3344444545444322   45789999999999999888887754

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.58  E-value=0.076  Score=39.84  Aligned_cols=89  Identities=12%  Similarity=0.153  Sum_probs=63.4

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQP--DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFL  188 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~  188 (256)
                      +...+...|++++|+..|....... ..|  ...+|..+-..|...|++++|...+++..+.  .|+ ..+++.+-..|.
T Consensus        41 ~g~~~~~~g~~~~A~~~~~~al~l~-~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~--~~~~~~~~~~la~i~~  117 (168)
T CHL00033         41 DGMSAQSEGEYAEALQNYYEAMRLE-IDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER--NPFLPQALNNMAVICH  117 (168)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcc-ccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHH
Confidence            4555667799999999999887653 222  2357888888999999999999999988764  233 345556655666


Q ss_pred             -------HcCChhHHHHHHHHH
Q 025225          189 -------KDGSPADAMNIYEDM  203 (256)
Q Consensus       189 -------~~g~~~~a~~~~~~M  203 (256)
                             +.|+++.|...+++-
T Consensus       118 ~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        118 YRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HhhHHHHHcccHHHHHHHHHHH
Confidence                   777877666666543

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.57  E-value=0.047  Score=45.51  Aligned_cols=132  Identities=12%  Similarity=0.133  Sum_probs=94.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHH-HHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTE-VIRGFLK  189 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~-li~~~~~  189 (256)
                      ++-+.+.-.-++++++-.++.++.-- ..-|.+.|| +-.+++..|.+.+|+++|-......++ |..+|-+ |-+.|.+
T Consensus       364 smAs~fFL~~qFddVl~YlnSi~sYF-~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~  440 (557)
T KOG3785|consen  364 SMASYFFLSFQFDDVLTYLNSIESYF-TNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIR  440 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh-cCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHh
Confidence            46666667778899998888888775 566666666 568889999999999999887664443 5667765 4567889


Q ss_pred             cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCccccc
Q 025225          190 DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYD  247 (256)
Q Consensus       190 ~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~  247 (256)
                      +++++-|+++|-+|...+-  .-.....+.+-|.+.+++--|.+  -..+...|++..|.
T Consensus       441 nkkP~lAW~~~lk~~t~~e--~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~pEnWe  498 (557)
T KOG3785|consen  441 NKKPQLAWDMMLKTNTPSE--RFSLLQLIANDCYKANEFYYAAKAFDELEILDPTPENWE  498 (557)
T ss_pred             cCCchHHHHHHHhcCCchh--HHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCccccC
Confidence            9999999998877765432  11223345567778887766665  34456677777664

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

Probab=96.56  E-value=0.085  Score=43.59  Aligned_cols=125  Identities=10%  Similarity=0.046  Sum_probs=82.9

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHH----HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLI----ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~----~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      .++..+-..|-+...+..|+..+ .+-.  ..-|--+|++-    .+-..++.++|.++|+...+..  ..++....++-
T Consensus       257 dTfllLskvY~ridQP~~AL~~~-~~gl--d~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~--~~nvEaiAcia  331 (478)
T KOG1129|consen  257 DTFLLLSKVYQRIDQPERALLVI-GEGL--DSFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLH--PINVEAIACIA  331 (478)
T ss_pred             hHHHHHHHHHHHhccHHHHHHHH-hhhh--hcCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcC--Cccceeeeeee
Confidence            34555567788888888887433 2221  22344444433    3344577888888888887775  56777777777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      ..|.-.++.+-|.+.+.++.+.|+. +...|+.+=-.|.-.+++|-++.-|.+-.
T Consensus       332 ~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf~RAl  385 (478)
T KOG1129|consen  332 VGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQRAL  385 (478)
T ss_pred             eccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHHHHHH
Confidence            7777888888888888888887774 55566666555556667777776666654

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

Probab=96.51  E-value=0.045  Score=39.09  Aligned_cols=55  Identities=7%  Similarity=0.147  Sum_probs=49.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCHhhHHHHHHHHHHcCC
Q 025225          138 YQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE-DLFPDSQTYTEVIRGFLKDGS  192 (256)
Q Consensus       138 ~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~g~  192 (256)
                      ..|+..+..+++.+|+..|++..|.++.+...+. ++.-+..+|..|+.-.-..-+
T Consensus        48 l~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   48 LYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999999999998875 888889999999998766543

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

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

Probab=96.49  E-value=0.097  Score=44.57  Aligned_cols=103  Identities=12%  Similarity=-0.055  Sum_probs=76.1

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      -..+...|++++|+..+ +...+.. -.+... .+-.++.+.|++++|+..++...+..  ..+...|..+-.+|...|+
T Consensus         9 a~~a~~~~~~~~Ai~~~-~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~--P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          9 AKEAFVDDDFALAVDLY-TQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELD--PSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHcCCHHHHHHHH-HHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHhCC
Confidence            34556789999998655 4443322 112222 35667888999999999999999886  5678889999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGF  187 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  187 (256)
                      +++|...|++..+.  .|+.......+.-|
T Consensus        86 ~~eA~~~~~~al~l--~P~~~~~~~~l~~~  113 (356)
T PLN03088         86 YQTAKAALEKGASL--APGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            99999999998873  46665555555433

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.44  E-value=0.081  Score=39.92  Aligned_cols=86  Identities=14%  Similarity=0.160  Sum_probs=65.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHH
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIL  218 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~l  218 (256)
                      ....|..+-..|...|++++|...|++..+..-.++  ...|..+-..|.+.|++++|...+.+..+... -+...+..+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l  112 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNP-KQPSALNNI  112 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHH
Confidence            445677778888899999999999999886432222  46788899999999999999999999887521 134555566


Q ss_pred             HHHhcCCCC
Q 025225          219 LKGLLPHPL  227 (256)
Q Consensus       219 i~~~~~~g~  227 (256)
                      ...|...|+
T Consensus       113 g~~~~~~g~  121 (172)
T PRK02603        113 AVIYHKRGE  121 (172)
T ss_pred             HHHHHHcCC
Confidence            666766665

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

Probab=96.42  E-value=0.33  Score=38.17  Aligned_cols=167  Identities=16%  Similarity=0.133  Sum_probs=127.1

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHH----HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLI----ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLII  150 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~----~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~  150 (256)
                      .+..+-..|-+.|..+.|-+.+-+.+.   +.|+...+++    .+|..|.+++|.+-|++-.....+.--..||..+--
T Consensus        71 a~~~~A~~Yq~~Ge~~~A~e~YrkAls---l~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~  147 (250)
T COG3063          71 AHLVRAHYYQKLGENDLADESYRKALS---LAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGL  147 (250)
T ss_pred             HHHHHHHHHHHcCChhhHHHHHHHHHh---cCCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHH
Confidence            556667788999999999766654443   3454444444    468999999999999999877645555678999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChH
Q 025225          151 ALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLR  229 (256)
Q Consensus       151 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~  229 (256)
                      +..+.|+.+.|...|++-.+..  |+ ..+.-.+-...-+.|+.-.|..++++-...+. ++..+.-.-|+---..|+-+
T Consensus       148 Cal~~gq~~~A~~~l~raL~~d--p~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~  224 (250)
T COG3063         148 CALKAGQFDQAEEYLKRALELD--PQFPPALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRA  224 (250)
T ss_pred             HHhhcCCchhHHHHHHHHHHhC--cCCChHHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHH
Confidence            9999999999999999988742  33 35566777788889999999999999988876 88888888888777888866


Q ss_pred             HHHH--hhhhhcCCCccccc
Q 025225          230 SKVK--KDFEELFPEKHAYD  247 (256)
Q Consensus       230 ~a~~--~~~~~~~p~~~~~~  247 (256)
                      .+-+  .-.....|....|-
T Consensus       225 ~a~~Y~~qL~r~fP~s~e~q  244 (250)
T COG3063         225 AAQRYQAQLQRLFPYSEEYQ  244 (250)
T ss_pred             HHHHHHHHHHHhCCCcHHHH
Confidence            6555  44455566655443

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

Probab=96.39  E-value=0.025  Score=45.67  Aligned_cols=83  Identities=14%  Similarity=0.258  Sum_probs=49.6

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCCh-hHH
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSP-ADA  196 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~-~~a  196 (256)
                      -.+|++--..+++-|.+-. +.|... |-...--|-+.  -+-+.+++++|...|+.||-.+=..||.++.+-+-. .+.
T Consensus       103 VerDl~vYk~LlnvfPKgk-fiP~nv-fQ~~F~HYP~Q--Q~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~  178 (406)
T KOG3941|consen  103 VERDLDVYKGLLNVFPKGK-FIPQNV-FQKVFLHYPQQ--QNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKV  178 (406)
T ss_pred             chhhHHHHHHHHHhCcccc-cccHHH-HHHHHhhCchh--hhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccHHHH
Confidence            3344444444555555554 555533 33333334333  355788888888888888888888888888877653 344


Q ss_pred             HHHHHHHH
Q 025225          197 MNIYEDMI  204 (256)
Q Consensus       197 ~~~~~~M~  204 (256)
                      .+++-.|.
T Consensus       179 ~Rm~yWmP  186 (406)
T KOG3941|consen  179 KRMLYWMP  186 (406)
T ss_pred             HHHHHhhh
Confidence            44444443

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

Probab=96.34  E-value=0.047  Score=48.05  Aligned_cols=112  Identities=13%  Similarity=0.143  Sum_probs=90.4

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHH
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAM  197 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~  197 (256)
                      ...+....++|-++....+..+|+..+..|=-.|--.|++++|.+.|+....  +.| |..+||-|=..++...+.++|+
T Consensus       407 ~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~--v~Pnd~~lWNRLGAtLAN~~~s~EAI  484 (579)
T KOG1125|consen  407 SSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQ--VKPNDYLLWNRLGATLANGNRSEEAI  484 (579)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHh--cCCchHHHHHHhhHHhcCCcccHHHH
Confidence            3456677788888776653568999999999999999999999999999887  346 6789999999999999999999


Q ss_pred             HHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          198 NIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       198 ~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +-|++-++....--..=|| |-=+|...|.+++|++
T Consensus       485 sAY~rALqLqP~yVR~RyN-lgIS~mNlG~ykEA~~  519 (579)
T KOG1125|consen  485 SAYNRALQLQPGYVRVRYN-LGISCMNLGAYKEAVK  519 (579)
T ss_pred             HHHHHHHhcCCCeeeeehh-hhhhhhhhhhHHHHHH
Confidence            9999988763322334455 4446788999999998

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.31  E-value=0.14  Score=37.89  Aligned_cols=93  Identities=12%  Similarity=0.089  Sum_probs=74.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      ++=.-+...|++++|..+|.-+....  .-+..-|-.|=.++-..|++++|...|........ -|...+-.+=.++...
T Consensus        40 ~~A~~ly~~G~l~~A~~~f~~L~~~D--p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~l  116 (157)
T PRK15363         40 RYAMQLMEVKEFAGAARLFQLLTIYD--AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLAC  116 (157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHc
Confidence            45555678899999999999988776  45666677777777888999999999999887653 3667777788888899


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |+.+.|.+.|+.-...
T Consensus       117 G~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        117 DNVCYAIKALKAVVRI  132 (157)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999999876543

>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=96.30  E-value=0.17  Score=45.13  Aligned_cols=123  Identities=23%  Similarity=0.308  Sum_probs=85.9

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .++-..|-..|+.++|++ +++.....  .|+..    +--+.+-+.|++.+|.+..+..++..  .-|.+.=+-....+
T Consensus       198 ~~lAqhyd~~g~~~~Al~-~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD--~~DRyiNsK~aKy~  272 (517)
T PF12569_consen  198 YFLAQHYDYLGDYEKALE-YIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELD--LADRYINSKCAKYL  272 (517)
T ss_pred             HHHHHHHHHhCCHHHHHH-HHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCC--hhhHHHHHHHHHHH
Confidence            344566778888888884 44544332  34433    34566778899999999999888887  67888888888888


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhH--------HHHHHHHHHcCChhHHHHHHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTY--------TEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~--------~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      .++|+.++|++++....+.+..|-...+        .-.-.+|.+.|++..|+.-|....
T Consensus       273 LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~  332 (517)
T PF12569_consen  273 LRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVL  332 (517)
T ss_pred             HHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            9999999999998888876554433222        344456777888877776655443

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 [], [].

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

Probab=96.18  E-value=0.035  Score=34.26  Aligned_cols=56  Identities=25%  Similarity=0.418  Sum_probs=46.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      -..+...|++++|.+.|++..+..  | +...+..+-..+.+.|++++|...|++..+.
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            356788899999999999998865  5 5677888888888999999999999988754

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

Probab=96.13  E-value=0.48  Score=46.40  Aligned_cols=115  Identities=12%  Similarity=0.166  Sum_probs=60.1

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---HhhHHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD---SQTYTEVIRGF  187 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~---~~t~~~li~~~  187 (256)
                      +|...|.+....++|-++++.|.+.  +.-....|...+..+.+..+.++|.+++++..+.  -|-   +....-.+..-
T Consensus      1535 ~L~~iy~k~ek~~~A~ell~~m~KK--F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqLE 1610 (1710)
T KOG1070|consen 1535 KLLGIYEKSEKNDEADELLRLMLKK--FGQTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQLE 1610 (1710)
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHH--hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHHH
Confidence            3566666666666666666666655  3445556666666666666666666666654432  122   11112222222


Q ss_pred             HHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          188 LKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       188 ~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      .+.|+.+++..+|+.....-. --...|+..|+.=.++|+.+.
T Consensus      1611 Fk~GDaeRGRtlfEgll~ayP-KRtDlW~VYid~eik~~~~~~ 1652 (1710)
T KOG1070|consen 1611 FKYGDAERGRTLFEGLLSAYP-KRTDLWSVYIDMEIKHGDIKY 1652 (1710)
T ss_pred             hhcCCchhhHHHHHHHHhhCc-cchhHHHHHHHHHHccCCHHH
Confidence            345555555555555544311 123456666666666665443

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.10  E-value=0.073  Score=33.58  Aligned_cols=56  Identities=18%  Similarity=0.167  Sum_probs=41.2

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      +.+.+.+++++|.++++.+.+.+  +.++..|...-..|...|++++|.+.|++..+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD--PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC--cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            45667777888888888777775  556667777777777778888888877777763

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.08  E-value=0.19  Score=45.03  Aligned_cols=132  Identities=13%  Similarity=0.027  Sum_probs=88.8

Q ss_pred             HHHHHHHc-----CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc--------CCHHHHHHHHHHHHhC-CCCCCH
Q 025225          112 VLIELERQ-----EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART--------GKMNEAMQVWESMRKE-DLFPDS  177 (256)
Q Consensus       112 li~~~~~~-----~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~--------g~~~~a~~~~~~m~~~-g~~p~~  177 (256)
                      .+++....     ++.++|..+|++..+..  .-+...|..+-.+|...        .++.++.+..++.... ....+.
T Consensus       343 ~lrg~~~~~~~~~~~~~~A~~lle~Ai~ld--P~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~al~~~~~~~  420 (517)
T PRK10153        343 FYQAHHYLNSGDAKSLNKASDLLEEILKSE--PDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVALPELNVLP  420 (517)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhhcccCcCCh
Confidence            56665432     24789999999998875  33445555554444322        1233444444443332 233355


Q ss_pred             hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCccccc
Q 025225          178 QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYD  247 (256)
Q Consensus       178 ~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~  247 (256)
                      ..|.++--.....|++++|...+++..+.+  |+...|..+-..|...|+.++|.+  .....+.|...||.
T Consensus       421 ~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt~~  490 (517)
T PRK10153        421 RIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENTLY  490 (517)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCchHH
Confidence            677777555666899999999999998886  688899999999999999999999  34455667666653

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

Probab=95.99  E-value=0.41  Score=38.21  Aligned_cols=123  Identities=15%  Similarity=0.034  Sum_probs=96.7

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH--H-HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV--A-VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~-li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ......+.|+..+|+..+. +. ...-++|+.  + +=-+|-+.|++++|..-|.+..+..  .-+...+|.+--.|.-.
T Consensus       106 ~gk~~~~~g~~~~A~~~~r-kA-~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~--~~~p~~~nNlgms~~L~  181 (257)
T COG5010         106 QGKNQIRNGNFGEAVSVLR-KA-ARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELA--PNEPSIANNLGMSLLLR  181 (257)
T ss_pred             HHHHHHHhcchHHHHHHHH-HH-hccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc--cCCchhhhhHHHHHHHc
Confidence            4667788999999986664 33 233445665  3 5556778999999999999999884  66788899999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          156 GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      |+.+.|+.++.+....+- -|...-..+.......|++++|..+-..-...
T Consensus       182 gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~i~~~e~~~  231 (257)
T COG5010         182 GDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAEDIAVQELLS  231 (257)
T ss_pred             CCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHhhccccccc
Confidence            999999999999887643 26667778888888999999999887654433

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.89  E-value=0.18  Score=37.86  Aligned_cols=92  Identities=13%  Similarity=0.085  Sum_probs=68.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC--CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHH
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP--DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIL  218 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~l  218 (256)
                      -...|..+...+...|++++|...|++.....-.|  ...+|..+-..|.+.|++++|...+++..+.. +....++..+
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~l  112 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNM  112 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHH
Confidence            45667778888888999999999999987653222  23578888899999999999999999887652 2234556666


Q ss_pred             HHHhc-------CCCChHHHHH
Q 025225          219 LKGLL-------PHPLLRSKVK  233 (256)
Q Consensus       219 i~~~~-------~~g~~~~a~~  233 (256)
                      ...+.       ..|++++|..
T Consensus       113 a~i~~~~~~~~~~~g~~~~A~~  134 (168)
T CHL00033        113 AVICHYRGEQAIEQGDSEIAEA  134 (168)
T ss_pred             HHHHHHhhHHHHHcccHHHHHH
Confidence            66666       7777775544

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

Probab=95.85  E-value=0.18  Score=46.88  Aligned_cols=111  Identities=18%  Similarity=0.216  Sum_probs=63.3

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHH--HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELE--RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~--~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      |-.....++..+|+...-+.+++.+-.+- ..++.++.  +.|..++|..+++.....+  ..|..|..++-..|...|.
T Consensus        16 i~d~ld~~qfkkal~~~~kllkk~Pn~~~-a~vLkaLsl~r~gk~~ea~~~Le~~~~~~--~~D~~tLq~l~~~y~d~~~   92 (932)
T KOG2053|consen   16 IYDLLDSSQFKKALAKLGKLLKKHPNALY-AKVLKALSLFRLGKGDEALKLLEALYGLK--GTDDLTLQFLQNVYRDLGK   92 (932)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHCCCcHH-HHHHHHHHHHHhcCchhHHHHHhhhccCC--CCchHHHHHHHHHHHHHhh
Confidence            44455566666666555444443332211 12455543  4566666666666666555  3466666666667777777


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPAD  195 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~  195 (256)
                      .++|..+|++..+.  .|+..-...+.-+|.+.+++.+
T Consensus        93 ~d~~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~  128 (932)
T KOG2053|consen   93 LDEAVHLYERANQK--YPSEELLYHLFMAYVREKSYKK  128 (932)
T ss_pred             hhHHHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHH
Confidence            77777777665542  3555556666666666655543

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

Probab=95.82  E-value=0.19  Score=48.97  Aligned_cols=148  Identities=13%  Similarity=0.111  Sum_probs=112.2

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccC-CCcH-HHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC---HHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLL-KMDI-VAVLIELERQEETILAVKIFDIIRKQDWYQPD---AYIYKDLI  149 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~-~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~~y~~li  149 (256)
                      .+..+...|.+....++|. .+++.|.++-- .+.+ ......+.+..+-++|.+++++..+.   -|-   +....-..
T Consensus      1532 V~~~L~~iy~k~ek~~~A~-ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~---lPk~eHv~~IskfA 1607 (1710)
T KOG1070|consen 1532 VHLKLLGIYEKSEKNDEAD-ELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKS---LPKQEHVEFISKFA 1607 (1710)
T ss_pred             HHHHHHHHHHHhhcchhHH-HHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh---cchhhhHHHHHHHH
Confidence            4455677888899999997 55566655433 3332 25788888999999999999987655   333   33444445


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCCh--hHHHHHHHHhcCCCC
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEE--LPFRILLKGLLPHPL  227 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~--~t~~~li~~~~~~g~  227 (256)
                      ..-.++|+.+.+..+|+..... .+--...|+..|+.=.+.|+.+.+..+|++....++.|-.  .-|.-.++.=-++|+
T Consensus      1608 qLEFk~GDaeRGRtlfEgll~a-yPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gd 1686 (1710)
T KOG1070|consen 1608 QLEFKYGDAERGRTLFEGLLSA-YPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGD 1686 (1710)
T ss_pred             HHHhhcCCchhhHHHHHHHHhh-CccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCc
Confidence            5556889999999999998874 1224678999999999999999999999999999887754  566777877777776

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

Probab=95.79  E-value=0.18  Score=41.12  Aligned_cols=82  Identities=18%  Similarity=0.232  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHh-----CCCCCChhHHHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIK-----SPDPPEELPFRI  217 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~-----~g~~p~~~t~~~  217 (256)
                      .+++.++..+..+|+++.+.+.++++....- -|...|..+|.+|.+.|+...|...|+.+.+     .|+.|...+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp-~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELDP-YDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            4667788888889999999999999887421 3788999999999999999999999988764     599999999988


Q ss_pred             HHHHhcCC
Q 025225          218 LLKGLLPH  225 (256)
Q Consensus       218 li~~~~~~  225 (256)
                      ..+...+.
T Consensus       233 y~~~~~~~  240 (280)
T COG3629         233 YEEILRQD  240 (280)
T ss_pred             HHHHhccc
Confidence            88885544

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

Probab=95.76  E-value=0.048  Score=50.82  Aligned_cols=107  Identities=17%  Similarity=0.188  Sum_probs=87.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE-DLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~  190 (256)
                      +=-.++..|++++|..||.+..+..  .-+..+|-.+-++|..+|++-.|.++|+...+. .-.-++...+.|-+++-++
T Consensus       652 IgiVLA~kg~~~~A~dIFsqVrEa~--~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~  729 (1018)
T KOG2002|consen  652 IGIVLAEKGRFSEARDIFSQVREAT--SDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEA  729 (1018)
T ss_pred             hhhhhhhccCchHHHHHHHHHHHHH--hhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHh
Confidence            4555678899999999999999886  445568999999999999999999999976654 5566888899999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      |.+.+|.+..-.-......-...-||..+-
T Consensus       730 ~~~~eak~~ll~a~~~~p~~~~v~FN~a~v  759 (1018)
T KOG2002|consen  730 GKLQEAKEALLKARHLAPSNTSVKFNLALV  759 (1018)
T ss_pred             hhHHHHHHHHHHHHHhCCccchHHhHHHHH
Confidence            999999999887776655555566765443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.69  E-value=0.11  Score=47.40  Aligned_cols=108  Identities=17%  Similarity=0.170  Sum_probs=80.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      .|.+-....++.+|+.+++.++.+.   .-+.-|.-+-..|+..|+++.|+++|-+--         .++--|..|.++|
T Consensus       738 aieaai~akew~kai~ildniqdqk---~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~  805 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQK---TASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAG  805 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhc---cccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccc
Confidence            5566667788999999999988775   344567888899999999999999997632         3567788999999


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++++|..+-.+.  .|-......|-+=..-+-++|++.+|-+
T Consensus       806 kw~da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeq  845 (1636)
T KOG3616|consen  806 KWEDAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQ  845 (1636)
T ss_pred             cHHHHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhh
Confidence            999998876553  3334455666666666666777666655

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

Probab=95.58  E-value=0.68  Score=43.99  Aligned_cols=129  Identities=14%  Similarity=0.053  Sum_probs=84.0

Q ss_pred             chhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHH------------------HHHHH
Q 025225           73 GKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKI------------------FDIIR  133 (256)
Q Consensus        73 ~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~------------------~~~m~  133 (256)
                      ...+..++..+...++++++....-.......-.+... .+--.+.+.++.+++..+                  .+.|.
T Consensus        31 ~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~~~~i~  110 (906)
T PRK14720         31 FKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHICDKIL  110 (906)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHHHHHHHHH
Confidence            34677788999899999999854432222222222222 111133344444444444                  33333


Q ss_pred             hcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          134 KQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       134 ~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      +.+   -+...+-++-.+|-+.|+.++|..+++++.+.. .-|....|-+-..|+.. ++++|.+++.+-.+.
T Consensus       111 ~~~---~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~  178 (906)
T PRK14720        111 LYG---ENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR  178 (906)
T ss_pred             hhh---hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH
Confidence            222   233567778888888899999999999999876 34788889999999988 999999888876654

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

Probab=95.50  E-value=0.31  Score=46.22  Aligned_cols=107  Identities=10%  Similarity=0.071  Sum_probs=65.9

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      ..+..+|....+.|.+++.+ .++.+..+....|.+. .||-+|++.+++.+-+++.        ..||......+=+-|
T Consensus      1134 s~y~eVi~~a~~~~~~edLv-~yL~MaRkk~~E~~id~eLi~AyAkt~rl~elE~fi--------~gpN~A~i~~vGdrc 1204 (1666)
T KOG0985|consen 1134 SNYLEVIDVASRTGKYEDLV-KYLLMARKKVREPYIDSELIFAYAKTNRLTELEEFI--------AGPNVANIQQVGDRC 1204 (1666)
T ss_pred             HHHHHHHHHHHhcCcHHHHH-HHHHHHHHhhcCccchHHHHHHHHHhchHHHHHHHh--------cCCCchhHHHHhHHH
Confidence            45666788888888888887 6666667777777776 4888888888887765543        235555555555555


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMN  198 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  198 (256)
                      ...|.++.|.-+|..         +.-|..|-..+...|+++.|.+
T Consensus      1205 f~~~~y~aAkl~y~~---------vSN~a~La~TLV~LgeyQ~AVD 1241 (1666)
T KOG0985|consen 1205 FEEKMYEAAKLLYSN---------VSNFAKLASTLVYLGEYQGAVD 1241 (1666)
T ss_pred             hhhhhhHHHHHHHHH---------hhhHHHHHHHHHHHHHHHHHHH
Confidence            555555555544432         2234444444444455444443

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

Probab=95.48  E-value=0.52  Score=41.10  Aligned_cols=89  Identities=21%  Similarity=0.250  Sum_probs=75.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      .+..=-..|++..|.++|+...+   ..|+...|++.|+.=.+....+.|.+++++..-  ++|++.+|---.+-=-++|
T Consensus       147 Y~ymEE~LgNi~gaRqiferW~~---w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g  221 (677)
T KOG1915|consen  147 YIYMEEMLGNIAGARQIFERWME---WEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHG  221 (677)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHc---CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcC
Confidence            44444567999999999996653   579999999999999999999999999999876  5699999988888888889


Q ss_pred             ChhHHHHHHHHHHh
Q 025225          192 SPADAMNIYEDMIK  205 (256)
Q Consensus       192 ~~~~a~~~~~~M~~  205 (256)
                      ++..|..+|.+..+
T Consensus       222 ~~~~aR~VyerAie  235 (677)
T KOG1915|consen  222 NVALARSVYERAIE  235 (677)
T ss_pred             cHHHHHHHHHHHHH
Confidence            98888888877654

>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=95.31  E-value=0.042  Score=35.34  Aligned_cols=61  Identities=20%  Similarity=0.359  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhC----C-CCCC-HhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKE----D-LFPD-SQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g-~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      .+|+.+-..|...|++++|.+.|++..+.    | -.|+ ..+++.+-..|...|++++|.+++++-
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            46677777777778888888777776642    1 1122 456677777777777777777777654

...

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

Probab=95.28  E-value=0.96  Score=39.58  Aligned_cols=126  Identities=17%  Similarity=0.166  Sum_probs=94.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      +-..|....+.++..+.|++..+..+-.||  +|-.--..+.-.+++++|..=|++..+.  .| +...|-.+-.+.-+.
T Consensus       366 ~a~~y~d~~~~~~~~~~F~~A~~ldp~n~d--vYyHRgQm~flL~q~e~A~aDF~Kai~L--~pe~~~~~iQl~~a~Yr~  441 (606)
T KOG0547|consen  366 RAAAYADENQSEKMWKDFNKAEDLDPENPD--VYYHRGQMRFLLQQYEEAIADFQKAISL--DPENAYAYIQLCCALYRQ  441 (606)
T ss_pred             HHHHHhhhhccHHHHHHHHHHHhcCCCCCc--hhHhHHHHHHHHHHHHHHHHHHHHHhhc--ChhhhHHHHHHHHHHHHH
Confidence            556678889999999999999988744444  5555555566677899999999998773  34 345555555555578


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh--hhhhcCCC
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK--DFEELFPE  242 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~--~~~~~~p~  242 (256)
                      +++++++..|++-.+. ++-.+..|+..-..+...+++++|.++  ....++|+
T Consensus       442 ~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~  494 (606)
T KOG0547|consen  442 HKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPR  494 (606)
T ss_pred             HHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccc
Confidence            8999999999998876 444567788888999999999999993  33444555

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

Probab=95.25  E-value=0.42  Score=39.01  Aligned_cols=100  Identities=21%  Similarity=0.324  Sum_probs=77.0

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCCh
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~  193 (256)
                      -+.+.+++++|+..|.+..+..  .-|.+-|..--.+|.+.|.++.|.+=-+...+  +.|. ..+|..|=.+|...|++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~--P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~  165 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELD--PTNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKY  165 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcH
Confidence            3567788999999999988875  67888888889999999999998877776665  3343 46788888899999999


Q ss_pred             hHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          194 ADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       194 ~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      ++|.+.|++-.+.  .|+-.+|-.=|+
T Consensus       166 ~~A~~aykKaLel--dP~Ne~~K~nL~  190 (304)
T KOG0553|consen  166 EEAIEAYKKALEL--DPDNESYKSNLK  190 (304)
T ss_pred             HHHHHHHHhhhcc--CCCcHHHHHHHH
Confidence            9999998875543  666666654443

>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=95.02  E-value=0.17  Score=31.52  Aligned_cols=61  Identities=20%  Similarity=0.312  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcC-ChhHHHHHHHHHH
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDG-SPADAMNIYEDMI  204 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g-~~~~a~~~~~~M~  204 (256)
                      +.+|..+=..+...|++++|...|++..+.  .| +...|..+=.+|.+.| ++++|.+.|++-.
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~--~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIEL--DPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHH--STTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            345555555566666666666666665553  23 3445555555555555 4666666655543

...

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.00  E-value=0.66  Score=37.72  Aligned_cols=85  Identities=22%  Similarity=0.241  Sum_probs=54.8

Q ss_pred             HHcCCHHHHHHHHHHHHhcCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HhhHHHHHHHHH
Q 025225          117 ERQEETILAVKIFDIIRKQDWYQPD----AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD----SQTYTEVIRGFL  188 (256)
Q Consensus       117 ~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~  188 (256)
                      .+.|++++|...|+.+.+..   |+    ...+--+-.+|...|++++|...|+.+.+.  .|+    ...+-.+...|-
T Consensus       154 ~~~~~y~~Ai~af~~fl~~y---P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~--yP~s~~~~dAl~klg~~~~  228 (263)
T PRK10803        154 QDKSRQDDAIVAFQNFVKKY---PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN--YPKSPKAADAMFKVGVIMQ  228 (263)
T ss_pred             HhcCCHHHHHHHHHHHHHHC---cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCcchhHHHHHHHHHHH
Confidence            44577888888888777663   22    245556667777778888888888877652  122    222333444555


Q ss_pred             HcCChhHHHHHHHHHHhC
Q 025225          189 KDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       189 ~~g~~~~a~~~~~~M~~~  206 (256)
                      ..|+.++|..+|++..+.
T Consensus       229 ~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        229 DKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HcCCHHHHHHHHHHHHHH
Confidence            677888888887776655

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.97  E-value=0.56  Score=38.48  Aligned_cols=151  Identities=14%  Similarity=0.053  Sum_probs=105.8

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCC-------------CCHH------
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQ-------------PDAY------  143 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~-------------p~~~------  143 (256)
                      -+.|+.++|++.|-....-.|..|-.. .+--+..+.|+...|++...++.++| ++             ||+.      
T Consensus       155 ykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy~~~qyasALk~iSEIieRG-~r~HPElgIGm~tegiDvrsvgNt~  233 (459)
T KOG4340|consen  155 YKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHYSSRQYASALKHISEIIERG-IRQHPELGIGMTTEGIDVRSVGNTL  233 (459)
T ss_pred             eccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHHhhhhHHHHHHHHHHHHHhh-hhcCCccCccceeccCchhcccchH
Confidence            578999999999987777889988765 66667778899999999999999888 32             3321      


Q ss_pred             --HHHHHHHH-------HHhcCCHHHHHHHHHHHHhC-CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChh
Q 025225          144 --IYKDLIIA-------LARTGKMNEAMQVWESMRKE-DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEEL  213 (256)
Q Consensus       144 --~y~~li~~-------~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~  213 (256)
                        .-..++.+       +-+.|+++.|.+-+-.|+-+ .-..|.+|...+--.=. .+++-+..+=+.-+.+.+.-| ..
T Consensus       234 ~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~nPfP-~E  311 (459)
T KOG4340|consen  234 VLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQNPFP-PE  311 (459)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcCCCC-hH
Confidence              12233333       34669999999999999753 44567777665432211 344555555555555554434 47


Q ss_pred             HHHHHHHHhcCCCChHHHHHhhhh
Q 025225          214 PFRILLKGLLPHPLLRSKVKKDFE  237 (256)
Q Consensus       214 t~~~li~~~~~~g~~~~a~~~~~~  237 (256)
                      ||..++--||++.-++-|.....+
T Consensus       312 TFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  312 TFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             HHHHHHHHHhhhHHHhHHHHHHhh
Confidence            899999999999988888775443

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.97  E-value=0.29  Score=42.39  Aligned_cols=58  Identities=12%  Similarity=0.117  Sum_probs=45.6

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDA----YIYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      .+=.+|.+.|++++|+..|++-.+..   |+.    .+|..+-.+|...|+.++|.+.+++..+.
T Consensus        80 NLG~AL~~lGryeEAIa~f~rALeL~---Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         80 NLGLSLFSKGRVKDALAQFETALELN---PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC---CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            46677888888888888888877664   443    45888888888888888888888888774

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

Probab=94.96  E-value=0.71  Score=40.94  Aligned_cols=143  Identities=17%  Similarity=0.066  Sum_probs=101.1

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHH---H-HHHcCCHHHHHHHHHHHHh----cCCCC-CCHHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLI---E-LERQEETILAVKIFDIIRK----QDWYQ-PDAYIYKD  147 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~---~-~~~~~~~~~a~~~~~~m~~----~~~~~-p~~~~y~~  147 (256)
                      +++-..|.+.++.+-|- .|+..  ..++-|+-.-+++   . ....+.+.+|...|+.-..    .+.-+ .-..+++.
T Consensus       384 LYlgmey~~t~n~kLAe-~Ff~~--A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~N  460 (611)
T KOG1173|consen  384 LYLGMEYMRTNNLKLAE-KFFKQ--ALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNN  460 (611)
T ss_pred             HHHHHHHHHhccHHHHH-HHHHH--HHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHh
Confidence            34455778888888884 66533  3344553321111   1 1235678888888886541    11011 13456788


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          148 LIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       148 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                      |=.+|.+.+.+++|...|++-... .+-|..|+.++=-.|...|+++.|.+.|.+-.  .+.|+..+.+.++..+...
T Consensus       461 LGH~~Rkl~~~~eAI~~~q~aL~l-~~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  461 LGHAYRKLNKYEEAIDYYQKALLL-SPKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLAIED  535 (611)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHc-CCCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHHHHh
Confidence            888999999999999999988764 23488899999999999999999999999854  5689999999888876655

>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=94.83  E-value=0.16  Score=31.56  Aligned_cols=56  Identities=23%  Similarity=0.219  Sum_probs=46.9

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHh
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG-KMNEAMQVWESMRK  170 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g-~~~~a~~~~~~m~~  170 (256)
                      =..+...|++++|+..|++..+..  +-+...|..+=.+|.+.| ++++|.+.|++..+
T Consensus        10 g~~~~~~~~~~~A~~~~~~ai~~~--p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen   10 GQIYFQQGDYEEAIEYFEKAIELD--PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHTTHHHHHHHHHHHHHHHS--TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            345677899999999999988886  567888888988999999 79999999988765

...

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.76  E-value=0.91  Score=32.76  Aligned_cols=85  Identities=12%  Similarity=0.091  Sum_probs=58.5

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH
Q 025225          110 VAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK  189 (256)
Q Consensus       110 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  189 (256)
                      ..+|..+.+.+..+.....++.+.+.+  ..++..+|.+|..|++.+ .++..+.+..      .++.+....+++-|-+
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~--~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~   81 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLN--SENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccC--ccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHH
Confidence            357777777788888888888887776  367778888888888764 3344444442      1345555567777777


Q ss_pred             cCChhHHHHHHHHH
Q 025225          190 DGSPADAMNIYEDM  203 (256)
Q Consensus       190 ~g~~~~a~~~~~~M  203 (256)
                      .+.++++..++.++
T Consensus        82 ~~l~~~~~~l~~k~   95 (140)
T smart00299       82 AKLYEEAVELYKKD   95 (140)
T ss_pred             cCcHHHHHHHHHhh
Confidence            77777777777665

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

Probab=94.65  E-value=0.13  Score=46.70  Aligned_cols=118  Identities=18%  Similarity=0.168  Sum_probs=87.6

Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQV  164 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~  164 (256)
                      .+++.++.+-+-..+.-..+.++.. .+=-+..+.++++.|.+-|.......  .-+...||.+=.+|.+.|+-.+|...
T Consensus       498 ~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~--Pd~~eaWnNls~ayi~~~~k~ra~~~  575 (777)
T KOG1128|consen  498 NKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLE--PDNAEAWNNLSTAYIRLKKKKRAFRK  575 (777)
T ss_pred             chhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcC--CCchhhhhhhhHHHHHHhhhHHHHHH
Confidence            4666777655555555454544432 34444457788999999999877654  44567899999999999999999999


Q ss_pred             HHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          165 WESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       165 ~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      +.+..+.+ .-+-..|-.-+-.-.+.|.+++|.+.+.+|.+.
T Consensus       576 l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~  616 (777)
T KOG1128|consen  576 LKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDL  616 (777)
T ss_pred             HHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHh
Confidence            99988866 445566777777788999999999999888753

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=94.55  E-value=0.47  Score=41.05  Aligned_cols=115  Identities=21%  Similarity=0.225  Sum_probs=77.3

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH-HHHhCCCCCCHhhH-HHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWE-SMRKEDLFPDSQTY-TEVIRGFLK  189 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~-~m~~~g~~p~~~t~-~~li~~~~~  189 (256)
                      .|+.-.+..-++.|..+|-+..+.|-+.|++..|+++|.-++ .|+..-|.++|+ -|+..   ||+..| +-.+.-+..
T Consensus       403 ~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f---~d~~~y~~kyl~fLi~  478 (660)
T COG5107         403 HLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKF---PDSTLYKEKYLLFLIR  478 (660)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhC---CCchHHHHHHHHHHHH
Confidence            667667777788888888888888766788888888888776 456677788887 45543   555444 455556667


Q ss_pred             cCChhHHHHHHHHHHhCCCCCC--hhHHHHHHHHhcCCCChHHH
Q 025225          190 DGSPADAMNIYEDMIKSPDPPE--ELPFRILLKGLLPHPLLRSK  231 (256)
Q Consensus       190 ~g~~~~a~~~~~~M~~~g~~p~--~~t~~~li~~~~~~g~~~~a  231 (256)
                      -++-+.|..+|+.-... +.-+  ...|..+|+-=..-|++..+
T Consensus       479 inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v  521 (660)
T COG5107         479 INDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNV  521 (660)
T ss_pred             hCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHH
Confidence            77777888888743322 1111  34677777777777766544

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=94.53  E-value=0.32  Score=44.59  Aligned_cols=108  Identities=15%  Similarity=0.163  Sum_probs=67.9

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      |.+......+.+|+ .+++....+......+ -+-..|+..|+++.|+++|.+--          .++..|..|.+.|++
T Consensus       739 ieaai~akew~kai-~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~----------~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAI-SILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEAD----------LFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhH-hHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcc----------hhHHHHHHHhccccH
Confidence            33344445555554 2333344443333333 36678889999999999886532          467789999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHH
Q 025225          159 NEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIY  200 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~  200 (256)
                      ++|.++-++...  -..+...|-+--.-+-+.|++.+|.+++
T Consensus       808 ~da~kla~e~~~--~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  808 EDAFKLAEECHG--PEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             HHHHHHHHHhcC--chhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            999999877543  2334455555555555566666665554

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=94.47  E-value=0.9  Score=38.05  Aligned_cols=81  Identities=12%  Similarity=0.164  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      .+-+.-|.-+...|....|.++-.+.+-    ||..-|-.-|.+|++.+++++-..+...      +=+++-|...++.|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fkv----~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~  247 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFKV----PDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEAC  247 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcCC----cHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHH
Confidence            3455667778889999999999888765    8999999999999999999988876542      22568999999999


Q ss_pred             cCCCChHHHHH
Q 025225          223 LPHPLLRSKVK  233 (256)
Q Consensus       223 ~~~g~~~~a~~  233 (256)
                      .+.|...+|..
T Consensus       248 ~~~~~~~eA~~  258 (319)
T PF04840_consen  248 LKYGNKKEASK  258 (319)
T ss_pred             HHCCCHHHHHH
Confidence            99999998887

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

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=94.43  E-value=0.48  Score=29.69  Aligned_cols=55  Identities=18%  Similarity=0.228  Sum_probs=45.3

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ..|.+.+++++|.++++.+...  .| +...|...=..|.+.|++++|.+.|++..+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALEL--DPDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHh--CcccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            5678889999999999999885  24 5566677777888899999999999998866

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

Probab=94.40  E-value=1.3  Score=40.10  Aligned_cols=146  Identities=11%  Similarity=0.079  Sum_probs=93.3

Q ss_pred             cCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHH----hcCC---------CCCCHHHHHH--HH
Q 025225           85 RFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIR----KQDW---------YQPDAYIYKD--LI  149 (256)
Q Consensus        85 ~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~----~~~~---------~~p~~~~y~~--li  149 (256)
                      ...+..+.++.++....++|+++-...+...|-.-...+-.+++.-.+.    ..|.         -+|++..|+.  ++
T Consensus       299 ~~eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~la  378 (700)
T KOG1156|consen  299 NGEELKEIVDKYLRPLLSKGVPSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLA  378 (700)
T ss_pred             CcchhHHHHHHHHHHHhhcCCCchhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHH
Confidence            4466777777888888888885433345444433222222222222222    1110         1677777765  46


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHh-hHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCCh
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFPDSQ-TYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLL  228 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~  228 (256)
                      ..|-+.|+++.|....+....+  .|+.+ -|-+=-+-+...|++++|..++++-.+.. .||...=+--..-..+.++.
T Consensus       379 qh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INsKcAKYmLrAn~i  455 (700)
T KOG1156|consen  379 QHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINSKCAKYMLRANEI  455 (700)
T ss_pred             HHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHHHHHHHHHHcccc
Confidence            7788899999999999987763  35542 23333477888999999999999877652 35555544566666778888


Q ss_pred             HHHHH
Q 025225          229 RSKVK  233 (256)
Q Consensus       229 ~~a~~  233 (256)
                      ++|.+
T Consensus       456 ~eA~~  460 (700)
T KOG1156|consen  456 EEAEE  460 (700)
T ss_pred             HHHHH
Confidence            88887

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.40  E-value=2.2  Score=34.49  Aligned_cols=129  Identities=12%  Similarity=0.065  Sum_probs=86.5

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHH-----HHHhcCCHHHHHHHHHHHHhCC-CCCCHhhHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLII-----ALARTGKMNEAMQVWESMRKED-LFPDSQTYTEVIR  185 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~-----~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~  185 (256)
                      |.+.-.+.||.+.|...|++..+.. -+.|-.+++.++.     .|...+++..|...|.+..... -.|-.+-=-+|+.
T Consensus       218 Lgr~~MQ~GD~k~a~~yf~~vek~~-~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcl  296 (366)
T KOG2796|consen  218 LGRISMQIGDIKTAEKYFQDVEKVT-QKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCL  296 (366)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHHHH-hhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCCCchhhhchHHHHH
Confidence            5555567899999999999887665 4677777776654     3455688999999999888742 1122222235666


Q ss_pred             HHHHcCChhHHHHHHHHHHhCCCCCChhHHHH-------HHH-HhcCCCChHHHHHhhhhhcCCCccc
Q 025225          186 GFLKDGSPADAMNIYEDMIKSPDPPEELPFRI-------LLK-GLLPHPLLRSKVKKDFEELFPEKHA  245 (256)
Q Consensus       186 ~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~-------li~-~~~~~g~~~~a~~~~~~~~~p~~~~  245 (256)
                      .|  .|+..+|...++.|++.  .|...+-++       |-+ +|..+-+.+.++.-...+..||.+.
T Consensus       297 lY--lg~l~DAiK~~e~~~~~--~P~~~l~es~~~nL~tmyEL~Ys~~~~~k~~l~~~ia~~~~d~f~  360 (366)
T KOG2796|consen  297 LY--LGKLKDALKQLEAMVQQ--DPRHYLHESVLFNLTTMYELEYSRSMQKKQALLEAVAGKEGDSFN  360 (366)
T ss_pred             HH--HHHHHHHHHHHHHHhcc--CCccchhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHhccCCCccc
Confidence            66  48899999999999887  344444443       333 4445556555666666777887653

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=94.37  E-value=0.57  Score=34.68  Aligned_cols=82  Identities=10%  Similarity=-0.026  Sum_probs=64.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhH-HHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCC
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFPDSQTY-TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPL  227 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~-~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~  227 (256)
                      -.-+...|++++|.++|+-...-  .|....| -.|=-.|-..|++++|.+.|........ -|+..+-.+-.++...|+
T Consensus        42 A~~ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG~  118 (157)
T PRK15363         42 AMQLMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACDN  118 (157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcCC
Confidence            34456789999999999998873  4655444 4444455568999999999999887763 577888889999999999


Q ss_pred             hHHHHH
Q 025225          228 LRSKVK  233 (256)
Q Consensus       228 ~~~a~~  233 (256)
                      .+.|.+
T Consensus       119 ~~~A~~  124 (157)
T PRK15363        119 VCYAIK  124 (157)
T ss_pred             HHHHHH
Confidence            999887

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

Probab=94.24  E-value=0.92  Score=41.04  Aligned_cols=189  Identities=14%  Similarity=0.046  Sum_probs=100.1

Q ss_pred             cccccCCchHHHHHHHHHhcCCC---------ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccccccc---
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS---------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLI---   72 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~---------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~---   72 (256)
                      .|-++|+.+.|..+|+.-.+.+.         |...-..=.++.+++.+     +++.+........+....+....   
T Consensus       396 lYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~A-----l~lm~~A~~vP~~~~~~~yd~~~pvQ  470 (835)
T KOG2047|consen  396 LYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAA-----LKLMRRATHVPTNPELEYYDNSEPVQ  470 (835)
T ss_pred             HHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHH-----HHHHHhhhcCCCchhhhhhcCCCcHH
Confidence            46788999999999998776654         22222222334444444     55444333222111111111100   


Q ss_pred             ------chhHHHHHHHhhcCCCcHHHHHHHHHHHhh-ccCCCcHHH-HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH-H
Q 025225           73 ------GKEALFVILGLKRFKDDEEKLQKFIKTHVL-RLLKMDIVA-VLIELERQEETILAVKIFDIIRKQDWYQPDA-Y  143 (256)
Q Consensus        73 ------~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~-li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~  143 (256)
                            ...|...+.---..|-++.. ..+++.+.. +...|.+.. .-..+-.+.-+++++++|+.-...- --|++ .
T Consensus       471 ~rlhrSlkiWs~y~DleEs~gtfest-k~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~LF-k~p~v~d  548 (835)
T KOG2047|consen  471 ARLHRSLKIWSMYADLEESLGTFEST-KAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGISLF-KWPNVYD  548 (835)
T ss_pred             HHHHHhHHHHHHHHHHHHHhccHHHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccC-CCccHHH
Confidence                  01222222211223333333 234444433 334444331 1112234456899999999877664 23444 4


Q ss_pred             HHHHHHHHHHhc---CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHH
Q 025225          144 IYKDLIIALART---GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDM  203 (256)
Q Consensus       144 ~y~~li~~~~~~---g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M  203 (256)
                      .||+-+.-+.+.   ..++.|..+|++..+ |++|...-  ++--.|++    .|....|+.++++-
T Consensus       549 iW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aK--tiyLlYA~lEEe~GLar~amsiyera  612 (835)
T KOG2047|consen  549 IWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAK--TIYLLYAKLEEEHGLARHAMSIYERA  612 (835)
T ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHH--HHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            677777666653   579999999999988 77665433  23333433    57778888888773

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

Probab=94.20  E-value=2.4  Score=36.48  Aligned_cols=144  Identities=12%  Similarity=0.093  Sum_probs=81.7

Q ss_pred             hhcCCCcHHHHHHHHHHHhh-ccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHH--HHHHHhcCCH
Q 025225           83 LKRFKDDEEKLQKFIKTHVL-RLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDL--IIALARTGKM  158 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~-~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~l--i~~~~~~g~~  158 (256)
                      +...+++++|+-.| +.... +....+++ -|+..|.-.|.+++|.-.-++..+.  +.-+..+.+.+  .-.+-...--
T Consensus       344 L~~~~R~~~A~IaF-R~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~--~~~sA~~LtL~g~~V~~~dp~~r  420 (564)
T KOG1174|consen  344 LIALERHTQAVIAF-RTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL--FQNSARSLTLFGTLVLFPDPRMR  420 (564)
T ss_pred             HHhccchHHHHHHH-HHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH--hhcchhhhhhhcceeeccCchhH
Confidence            34556666665333 22211 11222333 3666666666666666665554433  23333333332  1111112224


Q ss_pred             HHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          159 NEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++|.+++++-.+  +.|+- ..-+.+-.-+...|..+++..++++-...  .||....+.|-+-+...+++.++++
T Consensus       421 EKAKkf~ek~L~--~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~  492 (564)
T KOG1174|consen  421 EKAKKFAEKSLK--INPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAME  492 (564)
T ss_pred             HHHHHHHHhhhc--cCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHH
Confidence            566666665443  34553 23345555566778888888888876655  6888888888888888888888877

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

Probab=94.06  E-value=1.5  Score=39.92  Aligned_cols=212  Identities=14%  Similarity=0.053  Sum_probs=118.8

Q ss_pred             ccccccccCCchHHHHHHHHHhcCCC----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHH
Q 025225            2 ATRLFSRSKIPILASIVLQNLTKNPS----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEAL   77 (256)
Q Consensus         2 ~i~~~~~~~~~~~A~~l~~~m~~~~~----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~   77 (256)
                      |+..-.++..++.|..+|..-+..+.    |-.-.+--.-.++.+++     ++++++..+.-+..         ..-|.
T Consensus       624 avKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA-----~rllEe~lk~fp~f---------~Kl~l  689 (913)
T KOG0495|consen  624 AVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEA-----LRLLEEALKSFPDF---------HKLWL  689 (913)
T ss_pred             HHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHH-----HHHHHHHHHhCCch---------HHHHH
Confidence            34455666677777777776654332    22111111112333444     44443333221111         22233


Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+=..+-+.++.+.|.+.+..-.   ...|+..    .|-+.=-+.|.+-.|..+++.-...+  .-+...|-..|..=.
T Consensus       690 mlGQi~e~~~~ie~aR~aY~~G~---k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN--Pk~~~lwle~Ir~El  764 (913)
T KOG0495|consen  690 MLGQIEEQMENIEMAREAYLQGT---KKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN--PKNALLWLESIRMEL  764 (913)
T ss_pred             HHhHHHHHHHHHHHHHHHHHhcc---ccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC--CCcchhHHHHHHHHH
Confidence            33344455566665554333211   1223333    33344446678888999998887776  678888888888888


Q ss_pred             hcCCHHHHHHHHHHHHhC----C-------------------------CCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          154 RTGKMNEAMQVWESMRKE----D-------------------------LFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~----g-------------------------~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +.|..+.|..+..+..+.    |                         +.-|....-++-..|-...++++|.+.|.+-+
T Consensus       765 R~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Rav  844 (913)
T KOG0495|consen  765 RAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAV  844 (913)
T ss_pred             HcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999888888776655432    2                         11222222333334444566788888888877


Q ss_pred             hCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          205 KSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       205 ~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +.+ .-+..+|.-+..-+.++|.-++-.+
T Consensus       845 k~d-~d~GD~wa~fykfel~hG~eed~ke  872 (913)
T KOG0495|consen  845 KKD-PDNGDAWAWFYKFELRHGTEEDQKE  872 (913)
T ss_pred             ccC-CccchHHHHHHHHHHHhCCHHHHHH
Confidence            652 3355788888888888887665555

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

Probab=94.06  E-value=2.5  Score=40.42  Aligned_cols=57  Identities=12%  Similarity=0.140  Sum_probs=35.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      ++-.+|-+.|+.++|..+++++.+..  .-|+.+-|.+-..|+.. ++++|.+++.+...
T Consensus       121 ~LA~~Ydk~g~~~ka~~~yer~L~~D--~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~  177 (906)
T PRK14720        121 TLAEAYAKLNENKKLKGVWERLVKAD--RDNPEIVKKLATSYEEE-DKEKAITYLKKAIY  177 (906)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHH
Confidence            45556666666666666666666665  45666666666666666 66666655555443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=93.90  E-value=1.3  Score=36.06  Aligned_cols=91  Identities=13%  Similarity=0.133  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----hhHHHHHHHHHHcCChhHHHHHHHHHHhC--CCCCChhHH
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS----QTYTEVIRGFLKDGSPADAMNIYEDMIKS--PDPPEELPF  215 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~M~~~--g~~p~~~t~  215 (256)
                      ...|+..+..+.+.|++++|...|+.+.+.  .|+.    ..+-.+-..|...|++++|...|....+.  +-......+
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl  220 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAM  220 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHH
Confidence            466788887778889999999999999874  3554    35667778888999999999999999865  111123333


Q ss_pred             HHHHHHhcCCCChHHHHHh
Q 025225          216 RILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       216 ~~li~~~~~~g~~~~a~~~  234 (256)
                      -.+...+...|+.++|.+.
T Consensus       221 ~klg~~~~~~g~~~~A~~~  239 (263)
T PRK10803        221 FKVGVIMQDKGDTAKAKAV  239 (263)
T ss_pred             HHHHHHHHHcCCHHHHHHH
Confidence            4455567788999999883

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

Probab=93.81  E-value=2.2  Score=39.11  Aligned_cols=153  Identities=10%  Similarity=0.013  Sum_probs=104.7

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHH-HHHHH----------------------------HHcCCHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVA-VLIEL----------------------------ERQEETILA  125 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-li~~~----------------------------~~~~~~~~a  125 (256)
                      .|.-+|..|+..|+..+|- .+...-.++.-.|-.+. +.+..                            .+.++++++
T Consensus       426 mw~~vi~CY~~lg~~~kae-ei~~q~lek~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~  504 (777)
T KOG1128|consen  426 MWDPVILCYLLLGQHGKAE-EINRQELEKDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEA  504 (777)
T ss_pred             HHHHHHHHHHHhcccchHH-HHHHHHhcCCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHH
Confidence            5566788999999888875 44433333222222221 22221                            123556666


Q ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          126 VKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       126 ~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      .+.|+.-.+..  ..-..+|=.+=.+..+.++++.|.+-|.....  ..|| ...||.+=.+|.+.|+-.+|...+.+-.
T Consensus       505 ~~hle~sl~~n--plq~~~wf~~G~~ALqlek~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAl  580 (777)
T KOG1128|consen  505 DKHLERSLEIN--PLQLGTWFGLGCAALQLEKEQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEAL  580 (777)
T ss_pred             HHHHHHHhhcC--ccchhHHHhccHHHHHHhhhHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHh
Confidence            66666544443  33444555555566677899999999998776  4575 4789999999999999999999999988


Q ss_pred             hCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          205 KSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       205 ~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +-+ .-+...|....-...+-|.+++|++
T Consensus       581 Kcn-~~~w~iWENymlvsvdvge~eda~~  608 (777)
T KOG1128|consen  581 KCN-YQHWQIWENYMLVSVDVGEFEDAIK  608 (777)
T ss_pred             hcC-CCCCeeeechhhhhhhcccHHHHHH
Confidence            876 5556677777777788899999888

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

Probab=93.69  E-value=1.8  Score=40.55  Aligned_cols=130  Identities=18%  Similarity=0.209  Sum_probs=86.7

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH--HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCCh
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL--ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~--~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  193 (256)
                      ...++++.+|++-.+.+.+..   |+. .|...+.++  .+.|+.++|..+++.....+.. |..|...+-..|...|+.
T Consensus        19 ~ld~~qfkkal~~~~kllkk~---Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~   93 (932)
T KOG2053|consen   19 LLDSSQFKKALAKLGKLLKKH---PNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKL   93 (932)
T ss_pred             HhhhHHHHHHHHHHHHHHHHC---CCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhh
Confidence            345677888888888776654   332 344444444  4678888888888876665544 788888888888888888


Q ss_pred             hHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhh-hhcCCCcccccchhHh
Q 025225          194 ADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDF-EELFPEKHAYDPPEEI  252 (256)
Q Consensus       194 ~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~-~~~~p~~~~~~~li~~  252 (256)
                      ++|..+|++..+.  -|+......+..+|.+.+++.+.-+  |.. +...-+++.|=+.++.
T Consensus        94 d~~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~pk~~yyfWsV~Sl  153 (932)
T KOG2053|consen   94 DEAVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKNFPKRAYYFWSVISL  153 (932)
T ss_pred             hHHHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHH
Confidence            8888888886654  5677777788888888887766444  333 3333334444344443

>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=93.56  E-value=0.24  Score=31.70  Aligned_cols=59  Identities=15%  Similarity=0.116  Sum_probs=42.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhc----CCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          112 VLIELERQEETILAVKIFDIIRKQ----DWYQPD-AYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      +=..|...|++++|+..|++..+.    |.-.|+ ..+++.+-..|...|++++|.+.+++-.+
T Consensus        11 la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen   11 LARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            555677888888888888876532    211233 56788888888899999999999887653

...

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

Probab=93.51  E-value=3  Score=37.23  Aligned_cols=132  Identities=17%  Similarity=0.146  Sum_probs=97.1

Q ss_pred             HHHHHHHHhhcc--CCCcHHHHHHHH-HHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225           93 LQKFIKTHVLRL--LKMDIVAVLIEL-ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus        93 ~~~~~~~~~~~~--~~~~~~~li~~~-~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      .+.|++.....+  +.||+.+.|..+ --.|++++|...|+......  +-|-.+||-|=..++...+.++|++-|.+.+
T Consensus       414 ~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~--Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rAL  491 (579)
T KOG1125|consen  414 QELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVK--PNDYLLWNRLGATLANGNRSEEAISAYNRAL  491 (579)
T ss_pred             HHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcC--CchHHHHHHhhHHhcCCcccHHHHHHHHHHH
Confidence            345666566666  667777655554 45789999999999888775  5677899999999999999999999999988


Q ss_pred             hCCCCCCH--hhHHHHHHHHHHcCChhHHHHHHHHH---HhC------CCCCChhHHHHHHHHhcCCCChH
Q 025225          170 KEDLFPDS--QTYTEVIRGFLKDGSPADAMNIYEDM---IKS------PDPPEELPFRILLKGLLPHPLLR  229 (256)
Q Consensus       170 ~~g~~p~~--~t~~~li~~~~~~g~~~~a~~~~~~M---~~~------g~~p~~~t~~~li~~~~~~g~~~  229 (256)
                      +  ++|+-  +-||.-| +|...|.+++|...|=+-   .+.      +..++...|.+|=.++.-.++.|
T Consensus       492 q--LqP~yVR~RyNlgI-S~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D  559 (579)
T KOG1125|consen  492 Q--LQPGYVRVRYNLGI-SCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSD  559 (579)
T ss_pred             h--cCCCeeeeehhhhh-hhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCch
Confidence            7  56763  4566555 467899999999888653   332      23345567777766666555544

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=93.48  E-value=1.5  Score=39.43  Aligned_cols=89  Identities=18%  Similarity=0.112  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHH
Q 025225          123 ILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYED  202 (256)
Q Consensus       123 ~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  202 (256)
                      ..+.+.............+...|.++--.....|++++|...+++..+.+  |+...|..+-..|...|+.++|.+.+++
T Consensus       401 ~~a~~~~~~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~  478 (517)
T PRK10153        401 AALSTELDNIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYST  478 (517)
T ss_pred             HHHHHHHHHhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34444444433321024456788888666667899999999999998854  8889999999999999999999999998


Q ss_pred             HHhCCCCCChhHH
Q 025225          203 MIKSPDPPEELPF  215 (256)
Q Consensus       203 M~~~g~~p~~~t~  215 (256)
                      -...  .|...||
T Consensus       479 A~~L--~P~~pt~  489 (517)
T PRK10153        479 AFNL--RPGENTL  489 (517)
T ss_pred             HHhc--CCCCchH
Confidence            7665  4454454

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

Probab=93.43  E-value=1.1  Score=36.61  Aligned_cols=74  Identities=14%  Similarity=0.137  Sum_probs=66.8

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHhhHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK-----EDLFPDSQTYTEVIRG  186 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~li~~  186 (256)
                      ++.++...|+++.+.+.++++....  .-+...|..+|.+|.+.|+...|.+.|+++.+     .|+.|-..+.......
T Consensus       159 lae~~~~~~~~~~~~~~l~~Li~~d--p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~~~  236 (280)
T COG3629         159 LAEALIACGRADAVIEHLERLIELD--PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYEEI  236 (280)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHhcC--ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHHHH
Confidence            7788888999999999999999997  78999999999999999999999999999886     4899998888877776


Q ss_pred             H
Q 025225          187 F  187 (256)
Q Consensus       187 ~  187 (256)
                      .
T Consensus       237 ~  237 (280)
T COG3629         237 L  237 (280)
T ss_pred             h
Confidence            3

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.27  E-value=3.6  Score=33.06  Aligned_cols=103  Identities=20%  Similarity=0.285  Sum_probs=72.0

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHH
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMN  198 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  198 (256)
                      .|+.++|.++++.+.+..  +.|.++|--=|...-..|+--+|.+-+.+..+. +.-|...|.-+-.-|...|++++|.-
T Consensus        99 ~~~~~~A~e~y~~lL~dd--pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~f  175 (289)
T KOG3060|consen   99 TGNYKEAIEYYESLLEDD--PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAF  175 (289)
T ss_pred             hhchhhHHHHHHHHhccC--cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHH
Confidence            577888888888888776  677777776666666667767777777766653 45688888888888888888888888


Q ss_pred             HHHHHHhCCCCCCh-hHHHHHHHHhcCCC
Q 025225          199 IYEDMIKSPDPPEE-LPFRILLKGLLPHP  226 (256)
Q Consensus       199 ~~~~M~~~g~~p~~-~t~~~li~~~~~~g  226 (256)
                      .+++|.-.  .|.. .-|-.+-+.+.-.|
T Consensus       176 ClEE~ll~--~P~n~l~f~rlae~~Yt~g  202 (289)
T KOG3060|consen  176 CLEELLLI--QPFNPLYFQRLAEVLYTQG  202 (289)
T ss_pred             HHHHHHHc--CCCcHHHHHHHHHHHHHHh
Confidence            88888765  3333 33334555444444

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=93.22  E-value=0.034  Score=40.52  Aligned_cols=85  Identities=11%  Similarity=0.218  Sum_probs=57.3

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+|..+.+.+.++.....++.+.+.+ ..-+....|.++..|++.+..++..++++.       .+.+-...+++.|-+.
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~~~   83 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKEN-KENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCEKH   83 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTS-TC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHHTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcc-cccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHHhc
Confidence            46777777888888888888888776 456788888889999988877787777772       1223334555566666


Q ss_pred             CChhHHHHHHHHH
Q 025225          191 GSPADAMNIYEDM  203 (256)
Q Consensus       191 g~~~~a~~~~~~M  203 (256)
                      |.+++|.-++.++
T Consensus        84 ~l~~~a~~Ly~~~   96 (143)
T PF00637_consen   84 GLYEEAVYLYSKL   96 (143)
T ss_dssp             TSHHHHHHHHHCC
T ss_pred             chHHHHHHHHHHc
Confidence            6666666666554

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.

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

Probab=93.14  E-value=3  Score=34.14  Aligned_cols=92  Identities=11%  Similarity=0.013  Sum_probs=52.1

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART---GKMNEAMQVWESMRKEDLFP-DSQTYTEVIRG  186 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~---g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~  186 (256)
                      -|=..|...|+++.|..-|..-.+.-  .+++..+..+-.++...   ..-.++..+|+++...  .| |+..-.-|-..
T Consensus       161 ~Lg~~ym~~~~~~~A~~AY~~A~rL~--g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~--D~~~iral~lLA~~  236 (287)
T COG4235         161 LLGRAYMALGRASDALLAYRNALRLA--GDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL--DPANIRALSLLAFA  236 (287)
T ss_pred             HHHHHHHHhcchhHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc--CCccHHHHHHHHHH
Confidence            45566666666666666666666553  44555555554444433   2345566666666653  23 33334444445


Q ss_pred             HHHcCChhHHHHHHHHHHhC
Q 025225          187 FLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       187 ~~~~g~~~~a~~~~~~M~~~  206 (256)
                      +...|++.+|...|+.|.+.
T Consensus       237 afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         237 AFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHcccHHHHHHHHHHHHhc
Confidence            56666666666666666665

>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=93.11  E-value=1.1  Score=32.27  Aligned_cols=63  Identities=11%  Similarity=0.207  Sum_probs=26.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC
Q 025225          145 YKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD  208 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~  208 (256)
                      .+..++.+...|+-|.-.++..++.+ +-.|+....-.+-.+|.+.|+..++-+++.+.-+.|+
T Consensus        89 vD~ALd~lv~~~kkDqLdki~~~l~k-n~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   89 VDLALDILVKQGKKDQLDKIYNELKK-NEEINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHhh-ccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            34444444444555555555554443 1224444444444555555555555555554444443

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.07  E-value=1.7  Score=37.83  Aligned_cols=60  Identities=15%  Similarity=0.052  Sum_probs=42.9

Q ss_pred             chhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCc-------HHHHHHHHHHcCCHHHHHHHHHHHHhc
Q 025225           73 GKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMD-------IVAVLIELERQEETILAVKIFDIIRKQ  135 (256)
Q Consensus        73 ~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~li~~~~~~~~~~~a~~~~~~m~~~  135 (256)
                      ...+..+-.+|.+.|++++|+..+-+.+..   .|+       .+.+-.+|.+.|++++|++.+.+..+.
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL---~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALEL---NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh---CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            345666677888899999998655433322   343       235777888899999999999988865

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

Probab=93.04  E-value=0.71  Score=37.73  Aligned_cols=108  Identities=18%  Similarity=0.222  Sum_probs=81.8

Q ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHH
Q 025225          124 LAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYED  202 (256)
Q Consensus       124 ~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~  202 (256)
                      +....-++++..|             .-+.+.+++++|+..|.+..+  +.| |.+-|..=-.+|++.|+.+.|++=.+.
T Consensus        76 e~~~~AE~LK~eG-------------N~~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~  140 (304)
T KOG0553|consen   76 EDKALAESLKNEG-------------NKLMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCES  140 (304)
T ss_pred             hHHHHHHHHHHHH-------------HHHHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHHH
Confidence            4555566666666             345678999999999999887  445 567777888899999999999988777


Q ss_pred             HHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCccccc
Q 025225          203 MIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYD  247 (256)
Q Consensus       203 M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~  247 (256)
                      -.... .-...+|..|=.+|...|++++|++  .+.-.+.|+-.+|-
T Consensus       141 Al~iD-p~yskay~RLG~A~~~~gk~~~A~~aykKaLeldP~Ne~~K  186 (304)
T KOG0553|consen  141 ALSID-PHYSKAYGRLGLAYLALGKYEEAIEAYKKALELDPDNESYK  186 (304)
T ss_pred             HHhcC-hHHHHHHHHHHHHHHccCcHHHHHHHHHhhhccCCCcHHHH
Confidence            66541 1135678888889999999999998  45566677766653

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

Probab=92.89  E-value=3.2  Score=39.84  Aligned_cols=112  Identities=18%  Similarity=0.125  Sum_probs=67.2

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .|..+-.+-.+.+...+|++.+++     .-.|+.+ .+|+...+.|.+++-.+.+...++.. -.|.  .=+.||-+|+
T Consensus      1106 vWsqlakAQL~~~~v~dAieSyik-----adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~-~E~~--id~eLi~AyA 1177 (1666)
T KOG0985|consen 1106 VWSQLAKAQLQGGLVKDAIESYIK-----ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKV-REPY--IDSELIFAYA 1177 (1666)
T ss_pred             HHHHHHHHHHhcCchHHHHHHHHh-----cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhh-cCcc--chHHHHHHHH
Confidence            455555555556666666654431     1123333 47777777777777777766655554 3443  3356777777


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYE  201 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~  201 (256)
                      +.+++.+.+++..-       ||+.-...+=+-|...|.++.|.-+|.
T Consensus      1178 kt~rl~elE~fi~g-------pN~A~i~~vGdrcf~~~~y~aAkl~y~ 1218 (1666)
T KOG0985|consen 1178 KTNRLTELEEFIAG-------PNVANIQQVGDRCFEEKMYEAAKLLYS 1218 (1666)
T ss_pred             HhchHHHHHHHhcC-------CCchhHHHHhHHHhhhhhhHHHHHHHH
Confidence            77777766655432       666666666666666666666665554

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.76  E-value=1.6  Score=36.82  Aligned_cols=153  Identities=11%  Similarity=0.126  Sum_probs=101.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH--HHHHHH-----HH----cCCHHHHHHHHHHHHhcCCCCCCH-
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV--AVLIEL-----ER----QEETILAVKIFDIIRKQDWYQPDA-  142 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~li~~~-----~~----~~~~~~a~~~~~~m~~~~~~~p~~-  142 (256)
                      .-..++.-|.+++++++|.. +.++     +.|..-  =++.+.     .+    ...++-|.+.|+-.-+++ ..-|+ 
T Consensus       287 ARlNL~iYyL~q~dVqeA~~-L~Kd-----l~PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa-~ecDTI  359 (557)
T KOG3785|consen  287 ARLNLIIYYLNQNDVQEAIS-LCKD-----LDPTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESA-LECDTI  359 (557)
T ss_pred             hhhhheeeecccccHHHHHH-HHhh-----cCCCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccc-cccccc
Confidence            44455667889999999973 4332     334322  133332     22    124677888888777776 33333 


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHH-HHHHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFR-ILLKG  221 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~-~li~~  221 (256)
                      .--.++-+.+.-...+|+..-.++....-=..-|..-|| +-.+++..|+..+|.++|-+.....++ |..+|. .|.++
T Consensus       360 pGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArC  437 (557)
T KOG3785|consen  360 PGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARC  437 (557)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHH
Confidence            234456666677778899988888887654445566655 568889999999999999877655554 445554 66788


Q ss_pred             hcCCCChHHHHHhhh
Q 025225          222 LLPHPLLRSKVKKDF  236 (256)
Q Consensus       222 ~~~~g~~~~a~~~~~  236 (256)
                      |.++|..+-|.+|..
T Consensus       438 yi~nkkP~lAW~~~l  452 (557)
T KOG3785|consen  438 YIRNKKPQLAWDMML  452 (557)
T ss_pred             HHhcCCchHHHHHHH
Confidence            999999888888544

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

Probab=92.75  E-value=4.7  Score=33.03  Aligned_cols=121  Identities=16%  Similarity=0.099  Sum_probs=74.0

Q ss_pred             HHHHHHHc-CCHHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-----CHh--h
Q 025225          112 VLIELERQ-EETILAVKIFDIIRKQ----DWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-----DSQ--T  179 (256)
Q Consensus       112 li~~~~~~-~~~~~a~~~~~~m~~~----~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-----~~~--t  179 (256)
                      +=..|-.. |++++|.+.|++-.+.    |...--..++.-+...+.+.|++++|.++|++....-...     ++.  .
T Consensus       120 lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~  199 (282)
T PF14938_consen  120 LAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYF  199 (282)
T ss_dssp             HHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHH
Confidence            34445556 7999999999876533    3111123566777888899999999999999987653222     222  2


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHhC--CCCCC--hhHHHHHHHHhcCCC--ChHHHHH
Q 025225          180 YTEVIRGFLKDGSPADAMNIYEDMIKS--PDPPE--ELPFRILLKGLLPHP--LLRSKVK  233 (256)
Q Consensus       180 ~~~li~~~~~~g~~~~a~~~~~~M~~~--g~~p~--~~t~~~li~~~~~~g--~~~~a~~  233 (256)
                      ++++| .+...|++..|.+.|++....  ++..+  ......||.+|-...  .+.+++.
T Consensus       200 l~a~l-~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~  258 (282)
T PF14938_consen  200 LKAIL-CHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVA  258 (282)
T ss_dssp             HHHHH-HHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCH
T ss_pred             HHHHH-HHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            24444 445578999999999998754  44333  445567777776543  4444444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=92.65  E-value=4.5  Score=32.48  Aligned_cols=152  Identities=11%  Similarity=0.076  Sum_probs=96.4

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ...+.+.|+.++|+..| +.....--.+...     .+..++.+.+++++|...|++..+..+-.|+ .-|.-.+.+.+.
T Consensus        39 A~~~~~~g~y~~Ai~~f-~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~-~~~a~Y~~g~~~  116 (243)
T PRK10866         39 AQQKLQDGNWKQAITQL-EALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPN-IDYVLYMRGLTN  116 (243)
T ss_pred             HHHHHHCCCHHHHHHHH-HHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCc-hHHHHHHHHHhh
Confidence            44556789999998655 4444422222222     3677888999999999999999988633333 355555555442


Q ss_pred             --c---------------CC---HHHHHHHHHHHHhC----CCCCCHhhHH------------HHHHHHHHcCChhHHHH
Q 025225          155 --T---------------GK---MNEAMQVWESMRKE----DLFPDSQTYT------------EVIRGFLKDGSPADAMN  198 (256)
Q Consensus       155 --~---------------g~---~~~a~~~~~~m~~~----g~~p~~~t~~------------~li~~~~~~g~~~~a~~  198 (256)
                        .               .+   ..+|...|+++.+.    ...|+....-            .+-+-|-+.|.+.-|..
T Consensus       117 ~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~AA~~  196 (243)
T PRK10866        117 MALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVN  196 (243)
T ss_pred             hhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHH
Confidence              0               12   34555666666553    1222222211            23334788888888888


Q ss_pred             HHHHHHhC--CCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          199 IYEDMIKS--PDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       199 ~~~~M~~~--g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      -|+.+.+.  +-+......-.++++|.+.|..++|..
T Consensus       197 r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~  233 (243)
T PRK10866        197 RVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADK  233 (243)
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHH
Confidence            88888875  455566666788889988888887765

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=92.53  E-value=1.8  Score=31.20  Aligned_cols=56  Identities=14%  Similarity=0.193  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHH
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYE  201 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~  201 (256)
                      --..+|..+...+..+....+++.+...+. .+....|.+|..|++.+ .++..+++.
T Consensus         9 ~~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~-~~~ll~~l~   64 (140)
T smart00299        9 DVSEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYD-PQKEIERLD   64 (140)
T ss_pred             CHHHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHC-HHHHHHHHH
Confidence            345788888888999999999999988773 68889999999999864 455666666

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=92.43  E-value=1.4  Score=39.14  Aligned_cols=156  Identities=15%  Similarity=0.006  Sum_probs=95.4

Q ss_pred             cccccccCCchHHHHHHHHHhcCC-C-----------ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccccc
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNP-S-----------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKK   70 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~-~-----------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~   70 (256)
                      ++.++=+|+.+.+++++..-.+.+ +           |...+..+..... .......+..++..+...-|....+.+. 
T Consensus       195 l~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~-~~~~~~~a~~lL~~~~~~yP~s~lfl~~-  272 (468)
T PF10300_consen  195 LSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDG-EDVPLEEAEELLEEMLKRYPNSALFLFF-  272 (468)
T ss_pred             HhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcc-cCCCHHHHHHHHHHHHHhCCCcHHHHHH-
Confidence            345666789999999888765543 3           5555544443311 1222222366666666554444222211 


Q ss_pred             ccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHH
Q 025225           71 LIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIY  145 (256)
Q Consensus        71 ~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y  145 (256)
                              .-..+...|++++|++.+-+......--+...     -+.-.+.-.+++++|.+.|..+.+..  ..+..+|
T Consensus       273 --------~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s--~WSka~Y  342 (468)
T PF10300_consen  273 --------EGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES--KWSKAFY  342 (468)
T ss_pred             --------HHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc--ccHHHHH
Confidence                    12334678999999865543232111112221     36666788899999999999999886  6777777


Q ss_pred             HHHHHHH-HhcCCH-------HHHHHHHHHHHh
Q 025225          146 KDLIIAL-ARTGKM-------NEAMQVWESMRK  170 (256)
Q Consensus       146 ~~li~~~-~~~g~~-------~~a~~~~~~m~~  170 (256)
                      .-+..+| ...|+.       ++|.++|.+...
T Consensus       343 ~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  343 AYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            7775554 455767       889999988764

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=92.30  E-value=3.4  Score=30.24  Aligned_cols=47  Identities=11%  Similarity=0.218  Sum_probs=22.0

Q ss_pred             hhHHHHHHHHHHcCC-hhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC
Q 025225          178 QTYTEVIRGFLKDGS-PADAMNIYEDMIKSPDPPEELPFRILLKGLLP  224 (256)
Q Consensus       178 ~t~~~li~~~~~~g~-~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~  224 (256)
                      .+|++++.+.++..- ---+..+|+-|++.+.+++..-|..+|.++.+
T Consensus        80 ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~  127 (145)
T PF13762_consen   80 SSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALR  127 (145)
T ss_pred             chHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Confidence            345555555543333 22344445555554455555555555554443

>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=92.06  E-value=3.4  Score=29.78  Aligned_cols=62  Identities=18%  Similarity=0.193  Sum_probs=46.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLF  174 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~  174 (256)
                      ..|+.+.+.|.-++-.++++++.+.+  .+++...-.+-.+|.+-|+..++.+++.+..+.|++
T Consensus        91 ~ALd~lv~~~kkDqLdki~~~l~kn~--~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   91 LALDILVKQGKKDQLDKIYNELKKNE--EINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHH-------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHhccHHHHHHHHHHHhhcc--CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            36888888888888889999888765  788888888899999999999999999998888763

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

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

Probab=91.89  E-value=2.3  Score=38.11  Aligned_cols=118  Identities=14%  Similarity=0.117  Sum_probs=76.3

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHH----HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHH--HH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVA----VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKD--LI  149 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~--li  149 (256)
                      ..+-++.+...+++++|+... ......+  ||-.+    =+-++.+.+.+++|+.+.+.   .    +-..+++.  +=
T Consensus        15 l~t~ln~~~~~~e~e~a~k~~-~Kil~~~--pdd~~a~~cKvValIq~~ky~~ALk~ikk---~----~~~~~~~~~~fE   84 (652)
T KOG2376|consen   15 LLTDLNRHGKNGEYEEAVKTA-NKILSIV--PDDEDAIRCKVVALIQLDKYEDALKLIKK---N----GALLVINSFFFE   84 (652)
T ss_pred             HHHHHHHhccchHHHHHHHHH-HHHHhcC--CCcHhhHhhhHhhhhhhhHHHHHHHHHHh---c----chhhhcchhhHH
Confidence            344477788889999988555 3443333  55443    34455677888988844432   2    22233333  36


Q ss_pred             HHHH--hcCCHHHHHHHHHHHHhCCCCCCHh-hHHHHHHHHHHcCChhHHHHHHHHHHhCCC
Q 025225          150 IALA--RTGKMNEAMQVWESMRKEDLFPDSQ-TYTEVIRGFLKDGSPADAMNIYEDMIKSPD  208 (256)
Q Consensus       150 ~~~~--~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~M~~~g~  208 (256)
                      .+||  +.+..|+|...++     |+.++.. +-..=-.-+-+.|++++|+.+|..+.+++.
T Consensus        85 KAYc~Yrlnk~Dealk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~  141 (652)
T KOG2376|consen   85 KAYCEYRLNKLDEALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNS  141 (652)
T ss_pred             HHHHHHHcccHHHHHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC
Confidence            6776  4588999999888     3444433 444444456678999999999999988854

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

Probab=91.77  E-value=7.6  Score=35.36  Aligned_cols=121  Identities=14%  Similarity=0.183  Sum_probs=84.0

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHH----HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVL----IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li----~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+++..+-+.|+.+.|. .+++..  -+..|+.+-+-    +.+...|+++.|..++++..+..  .||...=.--..-.
T Consensus       375 y~laqh~D~~g~~~~A~-~yId~A--IdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD--~aDR~INsKcAKYm  449 (700)
T KOG1156|consen  375 YFLAQHYDKLGDYEVAL-EYIDLA--IDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD--TADRAINSKCAKYM  449 (700)
T ss_pred             HHHHHHHHHcccHHHHH-HHHHHH--hccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc--chhHHHHHHHHHHH
Confidence            34567778889888886 455543  34557666444    66788899999999999999887  77777666777777


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHH----------HHHHHcCChhHHHHHHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVI----------RGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li----------~~~~~~g~~~~a~~~~~~M~  204 (256)
                      .++++.++|.++.....+.|.  +...+-+-+          .+|.+.|++-.|+.=|....
T Consensus       450 LrAn~i~eA~~~~skFTr~~~--~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkfh~i~  509 (700)
T KOG1156|consen  450 LRANEIEEAEEVLSKFTREGF--GAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKFHEIE  509 (700)
T ss_pred             HHccccHHHHHHHHHhhhccc--chhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHHhhHH
Confidence            888999999999998888765  333332222          23556666666655554443

>PRK15331 chaperone protein SicA; Provisional

Probab=91.75  E-value=2.9  Score=31.21  Aligned_cols=89  Identities=13%  Similarity=-0.035  Sum_probs=66.4

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCCh
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  193 (256)
                      --+...|++++|..+|.-+.-.+  ..+..-|..|-.++-..+++++|...|...-..+. -|...+-..=..|...|+.
T Consensus        45 y~~y~~Gk~~eA~~~F~~L~~~d--~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~  121 (165)
T PRK15331         45 YEFYNQGRLDEAETFFRFLCIYD--FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKA  121 (165)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCH
Confidence            33457899999999999888776  34555567777777788999999999997665433 2333344455667788999


Q ss_pred             hHHHHHHHHHHh
Q 025225          194 ADAMNIYEDMIK  205 (256)
Q Consensus       194 ~~a~~~~~~M~~  205 (256)
                      +.|...|..-.+
T Consensus       122 ~~A~~~f~~a~~  133 (165)
T PRK15331        122 AKARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHHHh
Confidence            999999987766

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=91.73  E-value=3.7  Score=29.55  Aligned_cols=102  Identities=16%  Similarity=0.041  Sum_probs=74.2

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCH---hhHHHHHHHHHHc
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE-DLFPDS---QTYTEVIRGFLKD  190 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~---~t~~~li~~~~~~  190 (256)
                      +++..|+++.|++.|.+-...  +.-....||.--.++--.|+.++|.+=+++..+. |-+ +.   ..|..=-.-|-..
T Consensus        52 alaE~g~Ld~AlE~F~qal~l--~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg~lyRl~  128 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL--APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRGLLYRLL  128 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh--cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHh
Confidence            456789999999999998876  4668889999999999999999999999988874 432 22   2222222335567


Q ss_pred             CChhHHHHHHHHHHhCC----------CCCChhHHHHHH
Q 025225          191 GSPADAMNIYEDMIKSP----------DPPEELPFRILL  219 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g----------~~p~~~t~~~li  219 (256)
                      |+-+.|..=|+.-.+.|          +.|-...+|-|+
T Consensus       129 g~dd~AR~DFe~AA~LGS~FAr~QLV~lNPYAAlCN~ML  167 (175)
T KOG4555|consen  129 GNDDAARADFEAAAQLGSKFAREQLVELNPYAALCNQML  167 (175)
T ss_pred             CchHHHHHhHHHHHHhCCHHHHHHHHhcChHHHHHHHHH
Confidence            88888888887766655          445555555444

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=91.46  E-value=4.2  Score=29.62  Aligned_cols=43  Identities=14%  Similarity=0.097  Sum_probs=24.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ++.++.+.+++++|...+++..+.++-.| -+-|-..+.+++..
T Consensus        53 l~yayy~~~~y~~A~a~~~rFirLhP~hp-~vdYa~Y~~gL~~~   95 (142)
T PF13512_consen   53 LAYAYYKQGDYEEAIAAYDRFIRLHPTHP-NVDYAYYMRGLSYY   95 (142)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHhCCCCC-CccHHHHHHHHHHH
Confidence            66666666666666666666666652223 24455555555443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.34  E-value=6.6  Score=31.63  Aligned_cols=117  Identities=16%  Similarity=0.146  Sum_probs=72.0

Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHHH---HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIVA---VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAM  162 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~~---li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~  162 (256)
                      .|+.++|. .+++...+.. +.|..+   =|...-..|.-.+|++-+++..+.  +.-|...|--+-..|...|++++|.
T Consensus        99 ~~~~~~A~-e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~--F~~D~EAW~eLaeiY~~~~~f~kA~  174 (289)
T KOG3060|consen   99 TGNYKEAI-EYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK--FMNDQEAWHELAEIYLSEGDFEKAA  174 (289)
T ss_pred             hhchhhHH-HHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH--hcCcHHHHHHHHHHHHhHhHHHHHH
Confidence            45666665 3444444444 223331   222333345555777777777766  5778888888888888888888888


Q ss_pred             HHHHHHHhCCCCCCHhhHH-HHHHH---HHHcCChhHHHHHHHHHHhCCC
Q 025225          163 QVWESMRKEDLFPDSQTYT-EVIRG---FLKDGSPADAMNIYEDMIKSPD  208 (256)
Q Consensus       163 ~~~~~m~~~g~~p~~~t~~-~li~~---~~~~g~~~~a~~~~~~M~~~g~  208 (256)
                      =.++++.-  +.|....|. .+-..   -+...+.+-|...|.+-.+.+.
T Consensus       175 fClEE~ll--~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~  222 (289)
T KOG3060|consen  175 FCLEELLL--IQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNP  222 (289)
T ss_pred             HHHHHHHH--cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhCh
Confidence            88888876  346554443 22222   2223366678888888777633

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

Probab=91.24  E-value=7.7  Score=34.20  Aligned_cols=116  Identities=16%  Similarity=0.096  Sum_probs=91.8

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      .+.+=.++..+..|..+|+.....- ...| ..|--.+..=-..|++..|.++|++..+  ..||...|++.|..=.+-.
T Consensus       113 Yae~Emknk~vNhARNv~dRAvt~l-PRVd-qlWyKY~ymEE~LgNi~gaRqiferW~~--w~P~eqaW~sfI~fElRyk  188 (677)
T KOG1915|consen  113 YAEFEMKNKQVNHARNVWDRAVTIL-PRVD-QLWYKYIYMEEMLGNIAGARQIFERWME--WEPDEQAWLSFIKFELRYK  188 (677)
T ss_pred             HHHHHHhhhhHhHHHHHHHHHHHhc-chHH-HHHHHHHHHHHHhcccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhh
Confidence            5666678889999999999887663 2333 3344444555567999999999999887  5699999999999999999


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +++.|..++++.+--  .|+..+|--..+==-++|.+..+..
T Consensus       189 eieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~  228 (677)
T KOG1915|consen  189 EIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARS  228 (677)
T ss_pred             HHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHH
Confidence            999999999998765  4899998887777777777665544

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=91.15  E-value=5.7  Score=30.55  Aligned_cols=118  Identities=19%  Similarity=0.075  Sum_probs=90.4

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCCCHhhHHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE---DLFPDSQTYTEVIRGF  187 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~~t~~~li~~~  187 (256)
                      .|-+++...|+..+|...|++-..-- +-.|....-.+-.+....+++.+|...++.+-+.   +-.||.  --.+-+.|
T Consensus        94 rLa~al~elGr~~EA~~hy~qalsG~-fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~--~Ll~aR~l  170 (251)
T COG4700          94 RLANALAELGRYHEAVPHYQQALSGI-FAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDG--HLLFARTL  170 (251)
T ss_pred             HHHHHHHHhhhhhhhHHHHHHHhccc-cCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCc--hHHHHHHH
Confidence            58899999999999999999977443 7888888888888888999999999999988774   334443  33455778


Q ss_pred             HHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          188 LKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       188 ~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ...|+..+|..-|+.....  -|+..--.-.-.-+.+.|+.+++..
T Consensus       171 aa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~a  214 (251)
T COG4700         171 AAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANA  214 (251)
T ss_pred             HhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHH
Confidence            8889999999999988765  4444444444555677777676655

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=91.08  E-value=2  Score=29.23  Aligned_cols=87  Identities=15%  Similarity=0.162  Sum_probs=58.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHH
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIY  200 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~  200 (256)
                      .-++|..|-+++...+  .-...+--+-+..+.+.|++++|..+.+.+.    .||...|-+|-.+  +.|..+++..-+
T Consensus        20 cHqEA~tIAdwL~~~~--~~~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~----~pdlepw~ALce~--rlGl~s~l~~rl   91 (115)
T TIGR02508        20 CHQEANTIADWLHLKG--ESEEAVQLIRLSSLMNRGDYQSALQLGNKLC----YPDLEPWLALCEW--RLGLGSALESRL   91 (115)
T ss_pred             HHHHHHHHHHHHhcCC--chHHHHHHHHHHHHHccchHHHHHHhcCCCC----CchHHHHHHHHHH--hhccHHHHHHHH
Confidence            3577777777777555  1133333344566778888888888887774    4888888776543  677777777777


Q ss_pred             HHHHhCCCCCChhHHH
Q 025225          201 EDMIKSPDPPEELPFR  216 (256)
Q Consensus       201 ~~M~~~g~~p~~~t~~  216 (256)
                      .+|...| .|...+|.
T Consensus        92 ~rla~sg-~p~lq~Fa  106 (115)
T TIGR02508        92 NRLAASG-DPRLQTFV  106 (115)
T ss_pred             HHHHhCC-CHHHHHHH
Confidence            7887775 34445544

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.05  E-value=1.4  Score=36.34  Aligned_cols=119  Identities=10%  Similarity=0.037  Sum_probs=78.9

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHH-HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIE-LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~-~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ..+-+.+.+.+|+ .+...|...   |+..    .+=.+ ....+|+-.+..+.++....|    +..+-+..-...-+.
T Consensus        86 QSLY~A~i~ADAL-rV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en----~Ad~~in~gCllyke  157 (459)
T KOG4340|consen   86 QSLYKACIYADAL-RVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN----EADGQINLGCLLYKE  157 (459)
T ss_pred             HHHHHhcccHHHH-HHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC----ccchhccchheeecc
Confidence            4455666777776 343444321   2222    12111 234678888888888877655    333444444445688


Q ss_pred             CCHHHHHHHHHHHHhC-CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC
Q 025225          156 GKMNEAMQVWESMRKE-DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP  209 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  209 (256)
                      |.+++|.+-|++..+. |.. ....||.-+..|. .|+.+.|+....+..++|++
T Consensus       158 gqyEaAvqkFqaAlqvsGyq-pllAYniALaHy~-~~qyasALk~iSEIieRG~r  210 (459)
T KOG4340|consen  158 GQYEAAVQKFQAALQVSGYQ-PLLAYNLALAHYS-SRQYASALKHISEIIERGIR  210 (459)
T ss_pred             ccHHHHHHHHHHHHhhcCCC-chhHHHHHHHHHh-hhhHHHHHHHHHHHHHhhhh
Confidence            9999999999988875 665 4678999888875 58899999999998887643

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

Probab=90.80  E-value=0.76  Score=24.55  Aligned_cols=23  Identities=17%  Similarity=0.329  Sum_probs=12.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHH
Q 025225          145 YKDLIIALARTGKMNEAMQVWES  167 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~  167 (256)
                      |+.|-..|.+.|++++|.++|++
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            45555555666666666666655

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=90.22  E-value=13  Score=33.09  Aligned_cols=150  Identities=12%  Similarity=0.060  Sum_probs=94.4

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH--------HHHHHHHH----cCCHHHHHHHHHHHHhcCCCCCC
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV--------AVLIELER----QEETILAVKIFDIIRKQDWYQPD  141 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--------~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~  141 (256)
                      .....++....=.|+=+.++..+.......++.-...        .++..++.    ..+.+.|.++++++.++   -|+
T Consensus       189 p~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~---yP~  265 (468)
T PF10300_consen  189 PKVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR---YPN  265 (468)
T ss_pred             HHHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh---CCC
Confidence            3555556666667888888866655444444433322        13333333    45789999999999987   488


Q ss_pred             HHHHHHHHHH-HHhcCCHHHHHHHHHHHHhCC--C-CCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC-CCCCChhHHH
Q 025225          142 AYIYKDLIIA-LARTGKMNEAMQVWESMRKED--L-FPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS-PDPPEELPFR  216 (256)
Q Consensus       142 ~~~y~~li~~-~~~~g~~~~a~~~~~~m~~~g--~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-g~~p~~~t~~  216 (256)
                      ...|.-.-.- +...|++++|.+.|++.....  . +.....+=-+.-.+.-.+++++|.+.|.++.+. .+  +..+|.
T Consensus       266 s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~W--Ska~Y~  343 (468)
T PF10300_consen  266 SALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKW--SKAFYA  343 (468)
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcccc--HHHHHH
Confidence            8888766544 455699999999999765421  0 112233333444466689999999999999875 44  444554


Q ss_pred             HHHHHh-cCCCCh
Q 025225          217 ILLKGL-LPHPLL  228 (256)
Q Consensus       217 ~li~~~-~~~g~~  228 (256)
                      -+.-+| ...|+.
T Consensus       344 Y~~a~c~~~l~~~  356 (468)
T PF10300_consen  344 YLAAACLLMLGRE  356 (468)
T ss_pred             HHHHHHHHhhccc
Confidence            433333 355655

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=90.22  E-value=5.7  Score=29.04  Aligned_cols=97  Identities=12%  Similarity=0.123  Sum_probs=71.3

Q ss_pred             HhhccCCCcHH-----HHHHHHHHcCCHHHHHHHHHHHHhcCC----CCCCHHHHHHHHHHHHhcCC-HHHHHHHHHHHH
Q 025225          100 HVLRLLKMDIV-----AVLIELERQEETILAVKIFDIIRKQDW----YQPDAYIYKDLIIALARTGK-MNEAMQVWESMR  169 (256)
Q Consensus       100 ~~~~~~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~----~~p~~~~y~~li~~~~~~g~-~~~a~~~~~~m~  169 (256)
                      |.+.+..+++.     .+|+-.+.-+++....++++.+.....    -..+...|++++.+.++... ---+..+|+-|+
T Consensus        28 ~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk  107 (145)
T PF13762_consen   28 MQEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLK  107 (145)
T ss_pred             hhhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHH
Confidence            45556666665     366666777888888888888753320    03455689999999988877 455678999999


Q ss_pred             hCCCCCCHhhHHHHHHHHHHcCChhHHH
Q 025225          170 KEDLFPDSQTYTEVIRGFLKDGSPADAM  197 (256)
Q Consensus       170 ~~g~~p~~~t~~~li~~~~~~g~~~~a~  197 (256)
                      +.+.+++..-|..+|.++.+. ...+..
T Consensus       108 ~~~~~~t~~dy~~li~~~l~g-~~~~~~  134 (145)
T PF13762_consen  108 KNDIEFTPSDYSCLIKAALRG-YFHDSL  134 (145)
T ss_pred             HcCCCCCHHHHHHHHHHHHcC-CCCcch
Confidence            989999999999999997664 443333

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.77  E-value=4.7  Score=33.54  Aligned_cols=93  Identities=20%  Similarity=0.241  Sum_probs=60.3

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          113 LIELERQEETILAVKIFDIIRKQD--WYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~--~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      +..-....+++.++..+-.++++.  |..|+...|+ .+. ++-.-+.+++..++..=.+-|+-||..|++.+|+.+.+.
T Consensus        71 V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~-~ir-lllky~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~  148 (418)
T KOG4570|consen   71 VDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHT-WIR-LLLKYDPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKK  148 (418)
T ss_pred             hhccccccchhHHHHHHHHHhcCcchhhhccccHHH-HHH-HHHccChHHHHHHHhCcchhccccchhhHHHHHHHHHhc
Confidence            333334456777777777776553  1233322221 222 223345678888888777788888888888888888888


Q ss_pred             CChhHHHHHHHHHHhCC
Q 025225          191 GSPADAMNIYEDMIKSP  207 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g  207 (256)
                      ++..+|.++--.|...+
T Consensus       149 ~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  149 ENYKDAASVVTEVMMQE  165 (418)
T ss_pred             ccHHHHHHHHHHHHHHH
Confidence            88888888777766553

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

Probab=89.73  E-value=0.84  Score=24.38  Aligned_cols=26  Identities=19%  Similarity=0.370  Sum_probs=21.3

Q ss_pred             hHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          179 TYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       179 t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +|+.|=..|.+.|++++|.++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            47788889999999999999999854

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

Probab=89.63  E-value=10  Score=31.07  Aligned_cols=151  Identities=15%  Similarity=0.102  Sum_probs=90.4

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhh---ccCCCcHH-H---HHHHHHHcCCHHHHHHHHHHHH----hcCCCCCCH--HH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVL---RLLKMDIV-A---VLIELERQEETILAVKIFDIIR----KQDWYQPDA--YI  144 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~-~---li~~~~~~~~~~~a~~~~~~m~----~~~~~~p~~--~~  144 (256)
                      ..-+.|...+++++|.+.+.+....   .+-..+.. .   ....| +..++++|.+.+++..    +.|  .|+.  .+
T Consensus        40 ~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~-k~~~~~~Ai~~~~~A~~~y~~~G--~~~~aA~~  116 (282)
T PF14938_consen   40 KAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCY-KKGDPDEAIECYEKAIEIYREAG--RFSQAAKC  116 (282)
T ss_dssp             HHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH-HHTTHHHHHHHHHHHHHHHHHCT---HHHHHHH
T ss_pred             HHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-HhhCHHHHHHHHHHHHHHHHhcC--cHHHHHHH
Confidence            3456777888999888666544322   12211111 1   33334 4448888888888754    445  3333  46


Q ss_pred             HHHHHHHHHhc-CCHHHHHHHHHHHHhC----CCCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC-----CCCh
Q 025225          145 YKDLIIALART-GKMNEAMQVWESMRKE----DLFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD-----PPEE  212 (256)
Q Consensus       145 y~~li~~~~~~-g~~~~a~~~~~~m~~~----g~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~-----~p~~  212 (256)
                      +..+-..|-.. |++++|.+.|++..+.    | .+.  ..++..+...+.+.|++++|.++|++....-.     +++.
T Consensus       117 ~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~  195 (282)
T PF14938_consen  117 LKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSA  195 (282)
T ss_dssp             HHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhH
Confidence            66677777777 8999999999987652    3 221  35677888889999999999999999875422     2333


Q ss_pred             h--HHHHHHHHhcCCCChHHHHH
Q 025225          213 L--PFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       213 ~--t~~~li~~~~~~g~~~~a~~  233 (256)
                      .  .+.++| ++...|+.-.|-+
T Consensus       196 ~~~~l~a~l-~~L~~~D~v~A~~  217 (282)
T PF14938_consen  196 KEYFLKAIL-CHLAMGDYVAARK  217 (282)
T ss_dssp             HHHHHHHHH-HHHHTT-HHHHHH
T ss_pred             HHHHHHHHH-HHHHcCCHHHHHH
Confidence            2  234555 4444577666655

>PRK04841 transcriptional regulator MalT; Provisional

Probab=89.58  E-value=16  Score=35.25  Aligned_cols=151  Identities=13%  Similarity=-0.013  Sum_probs=93.0

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHHHHHHHHH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAYIYKDLII  150 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~~y~~li~  150 (256)
                      .+...|+.+++.. ..+......-..+..       .+-..+...|++++|...+.+....    |...+...+++.+-.
T Consensus       461 ~~~~~g~~~~A~~-~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~  539 (903)
T PRK04841        461 VAINDGDPEEAER-LAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSE  539 (903)
T ss_pred             HHHhCCCHHHHHH-HHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHH
Confidence            3456888888874 434433321111111       1334456789999999999887643    211112345555666


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC----CCC--C-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC--CCCC--ChhHHHHHH
Q 025225          151 ALARTGKMNEAMQVWESMRKE----DLF--P-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS--PDPP--EELPFRILL  219 (256)
Q Consensus       151 ~~~~~g~~~~a~~~~~~m~~~----g~~--p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~--g~~p--~~~t~~~li  219 (256)
                      .+...|++++|...+++....    +..  | ....+..+-..+...|++++|.+.+.+....  ...|  ....+..+.
T Consensus       540 ~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la  619 (903)
T PRK04841        540 ILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLA  619 (903)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHH
Confidence            778899999999998886652    221  1 2233445555566789999999999887543  1112  233444566


Q ss_pred             HHhcCCCChHHHHH
Q 025225          220 KGLLPHPLLRSKVK  233 (256)
Q Consensus       220 ~~~~~~g~~~~a~~  233 (256)
                      ..+...|+.++|.+
T Consensus       620 ~~~~~~G~~~~A~~  633 (903)
T PRK04841        620 KISLARGDLDNARR  633 (903)
T ss_pred             HHHHHcCCHHHHHH
Confidence            67778899888876

>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=89.41  E-value=0.13  Score=37.36  Aligned_cols=80  Identities=15%  Similarity=0.179  Sum_probs=57.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCC
Q 025225          147 DLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHP  226 (256)
Q Consensus       147 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g  226 (256)
                      .+|..|.+.+..+....+++.+...+-.-+....|.++..|++.+..++..++++.       .+..-...+++.|.+.|
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~~~~   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCEKHG   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHHhcc
Confidence            35677777888899999999999877667889999999999999988999988872       12233345556666666


Q ss_pred             ChHHHHH
Q 025225          227 LLRSKVK  233 (256)
Q Consensus       227 ~~~~a~~  233 (256)
                      .+++++.
T Consensus        85 l~~~a~~   91 (143)
T PF00637_consen   85 LYEEAVY   91 (143)
T ss_dssp             SHHHHHH
T ss_pred             hHHHHHH
Confidence            6555554

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.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.29  E-value=9.4  Score=30.91  Aligned_cols=89  Identities=17%  Similarity=0.182  Sum_probs=52.0

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCH-hhHHHHHHHHHHc
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDA---YIYKDLIIALARTGKMNEAMQVWESMRKE-DLFPDS-QTYTEVIRGFLKD  190 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~---~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~-~t~~~li~~~~~~  190 (256)
                      +.+.|++..|.+.|....+..  .-++   ..+=-|-.++...|++++|...|..+.+. .-.|-. ..+=-|-....+.
T Consensus       151 ~~ksgdy~~A~~~F~~fi~~Y--P~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l  228 (262)
T COG1729         151 LYKSGDYAEAEQAFQAFIKKY--PNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRL  228 (262)
T ss_pred             HHHcCCHHHHHHHHHHHHHcC--CCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHh
Confidence            345667777777777776653  2121   23334566777777777777777776653 222221 3344444455566


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |+.++|+.+|++..+.
T Consensus       229 ~~~d~A~atl~qv~k~  244 (262)
T COG1729         229 GNTDEACATLQQVIKR  244 (262)
T ss_pred             cCHHHHHHHHHHHHHH
Confidence            7777777777766554

>PF09477 Type_III_YscG: Bacterial type II secretion system chaperone protein (type_III_yscG); InterPro: IPR013348 YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion)

Probab=89.03  E-value=4.7  Score=27.77  Aligned_cols=87  Identities=17%  Similarity=0.197  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHH
Q 025225          120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNI  199 (256)
Q Consensus       120 ~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  199 (256)
                      ...++|..|.+++...+  .-..++--+-+..+.+.|++++|  +..-  .....||...|-+|-.  .+.|..+++...
T Consensus        20 HcH~EA~tIa~wL~~~~--~~~E~v~lIr~~sLmNrG~Yq~A--Ll~~--~~~~~pdL~p~~AL~a--~klGL~~~~e~~   91 (116)
T PF09477_consen   20 HCHQEANTIADWLEQEG--EMEEVVALIRLSSLMNRGDYQEA--LLLP--QCHCYPDLEPWAALCA--WKLGLASALESR   91 (116)
T ss_dssp             T-HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHTT-HHHH--HHHH--TTS--GGGHHHHHHHH--HHCT-HHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCC--cHHHHHHHHHHHHHHhhHHHHHH--HHhc--ccCCCccHHHHHHHHH--HhhccHHHHHHH
Confidence            35788889999888887  34444555556778888999998  2222  2234588888776644  378888888888


Q ss_pred             HHHHHhCCCCCChhHH
Q 025225          200 YEDMIKSPDPPEELPF  215 (256)
Q Consensus       200 ~~~M~~~g~~p~~~t~  215 (256)
                      +.++..+| .|....|
T Consensus        92 l~rla~~g-~~~~q~F  106 (116)
T PF09477_consen   92 LTRLASSG-SPELQAF  106 (116)
T ss_dssp             HHHHCT-S-SHHHHHH
T ss_pred             HHHHHhCC-CHHHHHH
Confidence            88887665 3333443

The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia, and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.; GO: 0009405 pathogenesis; PDB: 3PH0_D 2UWJ_G 2P58_C.

>PLN02789 farnesyltranstransferase

Probab=88.90  E-value=13  Score=31.24  Aligned_cols=137  Identities=7%  Similarity=0.020  Sum_probs=93.7

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHHH----HHHHHHHcC-CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIVA----VLIELERQE-ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----li~~~~~~~-~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ..+...+..++|+... .....  ..|+..+    -=..+...| ++++++..++++.+..  .-+..+|+..-..+.+.
T Consensus        45 a~l~~~e~serAL~lt-~~aI~--lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n--pknyqaW~~R~~~l~~l  119 (320)
T PLN02789         45 AVYASDERSPRALDLT-ADVIR--LNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN--PKNYQIWHHRRWLAEKL  119 (320)
T ss_pred             HHHHcCCCCHHHHHHH-HHHHH--HCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC--CcchHHhHHHHHHHHHc
Confidence            3455677888888433 44432  3455543    111233445 6899999999999886  56667788766666666


Q ss_pred             CCH--HHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC
Q 025225          156 GKM--NEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP  224 (256)
Q Consensus       156 g~~--~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~  224 (256)
                      |..  +++.++++++.+..- -|...|+..--.+.+.|+++++++.++++.+.+.. |...|+..-..+.+
T Consensus       120 ~~~~~~~el~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~  188 (320)
T PLN02789        120 GPDAANKELEFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITR  188 (320)
T ss_pred             CchhhHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHh
Confidence            653  778899988887432 37789998888888999999999999999987644 33555554444433

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

Probab=88.80  E-value=3.8  Score=27.95  Aligned_cols=46  Identities=15%  Similarity=0.201  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          124 LAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       124 ~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      +..+-++.+.... ..|++....+.+.+|-+-+++.-|.++|+..+.
T Consensus        28 e~rrglN~l~~~D-lVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~   73 (108)
T PF02284_consen   28 ELRRGLNNLFGYD-LVPEPKIIEAALRACRRVNDFALAVRILEGIKD   73 (108)
T ss_dssp             HHHHHHHHHTTSS-B---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccc-cCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3444445555555 566666666666666666666666666666554

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 ....

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=88.67  E-value=15  Score=32.57  Aligned_cols=78  Identities=17%  Similarity=0.116  Sum_probs=56.9

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--HhhHHHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD--SQTYTEVIRGFLK  189 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~  189 (256)
                      +=.++.+.|+.++|.+.|.+|.+.....-+......||.++...+.+.++..++.+-.+... |.  ..+|+..+--+-.
T Consensus       265 LAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~l-pkSAti~YTaALLkaRa  343 (539)
T PF04184_consen  265 LAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISL-PKSATICYTAALLKARA  343 (539)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccC-CchHHHHHHHHHHHHHh
Confidence            44445578999999999999987641223456888999999999999999999999754322 33  4678876644433


Q ss_pred             c
Q 025225          190 D  190 (256)
Q Consensus       190 ~  190 (256)
                      .
T Consensus       344 v  344 (539)
T PF04184_consen  344 V  344 (539)
T ss_pred             h
Confidence            3

The molecular function of this protein is uncertain.

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.31  E-value=3.4  Score=34.33  Aligned_cols=90  Identities=9%  Similarity=0.016  Sum_probs=64.9

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhh--ccCCCcHH--HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVL--RLLKMDIV--AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      +.--....+++++...+++.-..  ....|++.  ++++-+-+ -+.++++.+...=.+-| +-||-++++.+|+.+.+.
T Consensus        71 V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllk-y~pq~~i~~l~npIqYG-iF~dqf~~c~l~D~flk~  148 (418)
T KOG4570|consen   71 VDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLK-YDPQKAIYTLVNPIQYG-IFPDQFTFCLLMDSFLKK  148 (418)
T ss_pred             hhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHc-cChHHHHHHHhCcchhc-cccchhhHHHHHHHHHhc
Confidence            33334567778887655533211  22333332  56665554 45789999999989999 999999999999999999


Q ss_pred             CCHHHHHHHHHHHHhC
Q 025225          156 GKMNEAMQVWESMRKE  171 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~  171 (256)
                      +++.+|-++.-.|...
T Consensus       149 ~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  149 ENYKDAASVVTEVMMQ  164 (418)
T ss_pred             ccHHHHHHHHHHHHHH
Confidence            9999999888777654

>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=88.20  E-value=12  Score=32.89  Aligned_cols=108  Identities=14%  Similarity=0.114  Sum_probs=68.5

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHH-------HhcC---------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 025225          111 AVLIELERQEETILAVKIFDII-------RKQD---------WYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLF  174 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m-------~~~~---------~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~  174 (256)
                      .+++-+-+.|..+.|+++-.+-       .+.|         .-..+...|..|-....+.|+++-|++.|.+...    
T Consensus       300 ~i~~fL~~~G~~e~AL~~~~D~~~rFeLAl~lg~L~~A~~~a~~~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d----  375 (443)
T PF04053_consen  300 SIARFLEKKGYPELALQFVTDPDHRFELALQLGNLDIALEIAKELDDPEKWKQLGDEALRQGNIELAEECYQKAKD----  375 (443)
T ss_dssp             HHHHHHHHTT-HHHHHHHSS-HHHHHHHHHHCT-HHHHHHHCCCCSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT-----
T ss_pred             HHHHHHHHCCCHHHHHhhcCChHHHhHHHHhcCCHHHHHHHHHhcCcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC----
Confidence            3555555666666665553321       1222         1245788999999999999999999999988665    


Q ss_pred             CCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          175 PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       175 p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                           |..|.--|.-.|+.+.-..+.+.-.+.|-      +|.-..++.-.|+.++.++
T Consensus       376 -----~~~L~lLy~~~g~~~~L~kl~~~a~~~~~------~n~af~~~~~lgd~~~cv~  423 (443)
T PF04053_consen  376 -----FSGLLLLYSSTGDREKLSKLAKIAEERGD------INIAFQAALLLGDVEECVD  423 (443)
T ss_dssp             -----HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHHHHT-HHHHHH
T ss_pred             -----ccccHHHHHHhCCHHHHHHHHHHHHHccC------HHHHHHHHHHcCCHHHHHH
Confidence                 57777778888888777777766666642      5555555555566666555

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.

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=87.76  E-value=20  Score=32.18  Aligned_cols=149  Identities=11%  Similarity=0.067  Sum_probs=108.0

Q ss_pred             chhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC-cHH---HHHHHHHHcCCHHHHHHHHHH-HHhcCCCCCCHHHHHH
Q 025225           73 GKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM-DIV---AVLIELERQEETILAVKIFDI-IRKQDWYQPDAYIYKD  147 (256)
Q Consensus        73 ~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~---~li~~~~~~~~~~~a~~~~~~-m~~~~~~~p~~~~y~~  147 (256)
                      +-.|...++.-.+...++.|- .++.+..+.+..+ +++   ++|.-+ .++|.+-|.++|+- |++.|   -++.--..
T Consensus       366 tLv~~~~mn~irR~eGlkaaR-~iF~kaR~~~r~~hhVfVa~A~mEy~-cskD~~~AfrIFeLGLkkf~---d~p~yv~~  440 (656)
T KOG1914|consen  366 TLVYCQYMNFIRRAEGLKAAR-KIFKKAREDKRTRHHVFVAAALMEYY-CSKDKETAFRIFELGLKKFG---DSPEYVLK  440 (656)
T ss_pred             ceehhHHHHHHHHhhhHHHHH-HHHHHHhhccCCcchhhHHHHHHHHH-hcCChhHHHHHHHHHHHhcC---CChHHHHH
Confidence            335555677667777777775 6667888878777 444   355544 56789999999995 55444   34444466


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCH--hhHHHHHHHHHHcCChhHHHHHHHHHHhC-C--CCCChhHHHHHHHHh
Q 025225          148 LIIALARTGKMNEAMQVWESMRKEDLFPDS--QTYTEVIRGFLKDGSPADAMNIYEDMIKS-P--DPPEELPFRILLKGL  222 (256)
Q Consensus       148 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~li~~~~~~g~~~~a~~~~~~M~~~-g--~~p~~~t~~~li~~~  222 (256)
                      .++-+..-++=..+..+|++....++.||.  ..|..+|+-=..-|++.-+.++-+++... .  ..|...+-..+++.|
T Consensus       441 YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY  520 (656)
T KOG1914|consen  441 YLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRY  520 (656)
T ss_pred             HHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHH
Confidence            788889999999999999999988777664  88999999999999999999998887654 1  334444455566655


Q ss_pred             cCCC
Q 025225          223 LPHP  226 (256)
Q Consensus       223 ~~~g  226 (256)
                      .-.+
T Consensus       521 ~~~d  524 (656)
T KOG1914|consen  521 GILD  524 (656)
T ss_pred             hhcc
Confidence            5444

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=87.63  E-value=1.9  Score=23.27  Aligned_cols=27  Identities=22%  Similarity=0.303  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      .+++.|-..|...|++++|..++++..
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            355556666666666666666666554

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=87.62  E-value=6.3  Score=28.72  Aligned_cols=74  Identities=16%  Similarity=0.205  Sum_probs=46.7

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--HhhHHHHHHHHHHcC
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQ-PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD--SQTYTEVIRGFLKDG  191 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~-p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~g  191 (256)
                      ..+.|++++|.+.|+.+..+-... -....-=-++.+|-+.+++++|...+++..+..  |+  -+-|--.+.|++.-.
T Consensus        20 ~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLh--P~hp~vdYa~Y~~gL~~~~   96 (142)
T PF13512_consen   20 ALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLH--PTHPNVDYAYYMRGLSYYE   96 (142)
T ss_pred             HHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCCCccHHHHHHHHHHHH
Confidence            346677888888888877663221 223444556777778888888888887777742  33  255666666665533

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=87.50  E-value=6  Score=26.72  Aligned_cols=44  Identities=14%  Similarity=0.226  Sum_probs=24.0

Q ss_pred             HHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225          125 AVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus       125 a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      +.+-++.+.... ..|++..-++.+.+|-+-+++.-|.++|+..+
T Consensus        26 ~rr~mN~l~~~D-lVP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          26 LRRGLNNLFGYD-LVPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             HHHHHHHHhccc-cCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            333444444444 55555555666666655566666666665554

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=87.42  E-value=15  Score=30.43  Aligned_cols=134  Identities=11%  Similarity=0.184  Sum_probs=84.3

Q ss_pred             HHHHHHHcCC-----HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh--c----CCHHHHHHHHHHHHhCC---CCCCH
Q 025225          112 VLIELERQEE-----TILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR--T----GKMNEAMQVWESMRKED---LFPDS  177 (256)
Q Consensus       112 li~~~~~~~~-----~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~--~----g~~~~a~~~~~~m~~~g---~~p~~  177 (256)
                      +...++-.++     +++...+++.|.+.| ++-+..+|=+.......  .    ....+|.++|+.|++.-   -.++-
T Consensus        63 la~~l~~~~~~p~~~~~~~~~~y~~L~~~g-Fk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D  141 (297)
T PF13170_consen   63 LAALLDISFEDPEEAFKEVLDIYEKLKEAG-FKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPED  141 (297)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHHHhc-cCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccc
Confidence            4444444444     577888999999999 99888777664333333  2    34778899999999862   33566


Q ss_pred             hhHHHHHHHHHHcCC----hhHHHHHHHHHHhCCCCCChh-HHHHHHHHhcCCCChHH---HHH----hhhhhcCCCccc
Q 025225          178 QTYTEVIRGFLKDGS----PADAMNIYEDMIKSPDPPEEL-PFRILLKGLLPHPLLRS---KVK----KDFEELFPEKHA  245 (256)
Q Consensus       178 ~t~~~li~~~~~~g~----~~~a~~~~~~M~~~g~~p~~~-t~~~li~~~~~~g~~~~---a~~----~~~~~~~p~~~~  245 (256)
                      +.+..|+..  ..++    .+++..+|+.+.+.|+..+-. .+-+-|-+++....-++   ..+    ....++++-...
T Consensus       142 ~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~  219 (297)
T PF13170_consen  142 YPFAALLAM--TSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMH  219 (297)
T ss_pred             hhHHHHHhc--ccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCcccccc
Confidence            788888776  3333    466788899999988865332 33333334443332222   222    455666666555


Q ss_pred             ccc
Q 025225          246 YDP  248 (256)
Q Consensus       246 ~~~  248 (256)
                      |.+
T Consensus       220 yp~  222 (297)
T PF13170_consen  220 YPT  222 (297)
T ss_pred             ccH
Confidence            653

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=87.33  E-value=1.8  Score=24.24  Aligned_cols=28  Identities=21%  Similarity=0.186  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      +|..+-..|...|++++|.++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4556666777777777777777777663

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=87.32  E-value=12  Score=32.91  Aligned_cols=153  Identities=14%  Similarity=0.066  Sum_probs=99.5

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH--h
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA--R  154 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~--~  154 (256)
                      -++++..++-..|.+...+..-.|...       -+|+||... +++.......+..+..   | ...|-.+..+..  +
T Consensus        17 qkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~~---~-~s~~l~LF~~L~~Y~   91 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQF---G-KSAYLPLFKALVAYK   91 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHhc---C-CchHHHHHHHHHHHH
Confidence            456777777555544444433334333       388888654 4777777777777663   3 344555655554  5


Q ss_pred             cCCHHHHHHHHHHHHhC--CCC------------CCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCChhHHH
Q 025225          155 TGKMNEAMQVWESMRKE--DLF------------PDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPEELPFR  216 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~--g~~------------p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~~~t~~  216 (256)
                      .+++++|.+.+......  +-.            +|-.-=+..+..+...|.+.++..++++|...    ...-+..+||
T Consensus        92 ~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd  171 (549)
T PF07079_consen   92 QKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYD  171 (549)
T ss_pred             hhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHH
Confidence            68899999988887764  322            23333467778888999999999999988754    4457999999


Q ss_pred             HHHHHhcCCCChHHHHHhhhhhcCCC
Q 025225          217 ILLKGLLPHPLLRSKVKKDFEELFPE  242 (256)
Q Consensus       217 ~li~~~~~~g~~~~a~~~~~~~~~p~  242 (256)
                      .++-.+++.=. =|..+.....+.||
T Consensus       172 ~~vlmlsrSYf-LEl~e~~s~dl~pd  196 (549)
T PF07079_consen  172 RAVLMLSRSYF-LELKESMSSDLYPD  196 (549)
T ss_pred             HHHHHHhHHHH-HHHHHhcccccChH
Confidence            98888877533 33445444555554

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=86.72  E-value=5.1  Score=27.72  Aligned_cols=27  Identities=15%  Similarity=0.384  Sum_probs=25.0

Q ss_pred             hHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          179 TYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       179 t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      -|+.|+.-|-..|..++|.+++.+..+
T Consensus        41 ~~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen   41 KYQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             CHHHHHHHHHccCccHHHHHHHHHHhc
Confidence            489999999999999999999999887

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=86.56  E-value=3.9  Score=22.78  Aligned_cols=36  Identities=17%  Similarity=0.137  Sum_probs=27.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDL  148 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~l  148 (256)
                      .+=.+|...|++++|.++|++..+..  .-|...|..+
T Consensus         6 ~la~~~~~~G~~~~A~~~~~~~l~~~--P~~~~a~~~L   41 (44)
T PF13428_consen    6 ALARAYRRLGQPDEAERLLRRALALD--PDDPEAWRAL   41 (44)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC--cCCHHHHHHh
Confidence            46678889999999999999999885  4455554443

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=86.42  E-value=6.1  Score=31.14  Aligned_cols=72  Identities=11%  Similarity=-0.037  Sum_probs=38.6

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcC-CCCCCHHHHHHHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQD-WYQPDAYIYKDLIIA  151 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~-~~~p~~~~y~~li~~  151 (256)
                      ++.+.+.+...+++....+..+.+.-..+.. -++..+|-.|++++|..-++-.-+.. ...+-..+|..+|.+
T Consensus         8 ~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           8 ISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             HHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            5566667777777655544444333322333 36777777777777766555443221 023444555555543

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

Probab=86.36  E-value=11  Score=33.40  Aligned_cols=56  Identities=21%  Similarity=0.106  Sum_probs=26.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPD-AYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      =..+|++.|++++|++=-.+-.+..   |+ .-.|+-.=.++...|++++|..-|.+=.+
T Consensus        42 rsaa~a~~~~~~~al~da~k~~~l~---p~w~kgy~r~Gaa~~~lg~~~eA~~ay~~GL~   98 (539)
T KOG0548|consen   42 RSAAYASLGSYEKALKDATKTRRLN---PDWAKGYSRKGAALFGLGDYEEAILAYSEGLE   98 (539)
T ss_pred             hHHHHHHHhhHHHHHHHHHHHHhcC---CchhhHHHHhHHHHHhcccHHHHHHHHHHHhh
Confidence            4455555555555554444444332   22 23444444444445555555555554333

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.35  E-value=12  Score=34.83  Aligned_cols=103  Identities=17%  Similarity=0.115  Sum_probs=85.3

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      --+.-+...|+..+|.++-.+.+     .||-..|=.=+.+++..+++++-+++-++++.      .+-|--.+.+|.+.
T Consensus       689 dTv~~li~~g~~k~a~ql~~~Fk-----ipdKr~~wLk~~aLa~~~kweeLekfAkskks------PIGy~PFVe~c~~~  757 (829)
T KOG2280|consen  689 DTVTTLILIGQNKRAEQLKSDFK-----IPDKRLWWLKLTALADIKKWEELEKFAKSKKS------PIGYLPFVEACLKQ  757 (829)
T ss_pred             HHHHHHHHccchHHHHHHHHhcC-----CcchhhHHHHHHHHHhhhhHHHHHHHHhccCC------CCCchhHHHHHHhc
Confidence            45667778899999988877776     79999999999999999999999888777653      45677788999999


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |+.++|..++.+....      .   -.+.+|.+.|++.+|.+
T Consensus       758 ~n~~EA~KYiprv~~l------~---ekv~ay~~~~~~~eAad  791 (829)
T KOG2280|consen  758 GNKDEAKKYIPRVGGL------Q---EKVKAYLRVGDVKEAAD  791 (829)
T ss_pred             ccHHHHhhhhhccCCh------H---HHHHHHHHhccHHHHHH
Confidence            9999999998763221      1   57889999999999888

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=86.23  E-value=13  Score=29.75  Aligned_cols=75  Identities=16%  Similarity=0.210  Sum_probs=51.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHH---HHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHhhHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYK---DLIIALARTGKMNEAMQVWESMRKED-LFPDSQTYTEVIRG  186 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~---~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~  186 (256)
                      ..-..+...|++++|.+.|+++....  +-+...-.   .+..+|-+.+++++|...|++..+.- -.|+ .-|.-.+.|
T Consensus        37 ~~A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~-~~~a~Y~~g  113 (243)
T PRK10866         37 ATAQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPN-IDYVLYMRG  113 (243)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCc-hHHHHHHHH
Confidence            34455567899999999999999875  22333332   34577789999999999999998752 2222 344445555


Q ss_pred             HH
Q 025225          187 FL  188 (256)
Q Consensus       187 ~~  188 (256)
                      .+
T Consensus       114 ~~  115 (243)
T PRK10866        114 LT  115 (243)
T ss_pred             Hh
Confidence            44

>PRK04841 transcriptional regulator MalT; Provisional

Probab=86.21  E-value=14  Score=35.72  Aligned_cols=117  Identities=11%  Similarity=-0.012  Sum_probs=78.6

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCC-C--CHhhHHHHHHH
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDA----YIYKDLIIALARTGKMNEAMQVWESMRKE--DLF-P--DSQTYTEVIRG  186 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~y~~li~~~~~~g~~~~a~~~~~~m~~~--g~~-p--~~~t~~~li~~  186 (256)
                      +...|++++|...+++..+.- ...+.    ...+.+-..+...|++++|...+++....  ... +  -..+++.+-..
T Consensus       462 ~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        462 AINDGDPEEAERLAELALAEL-PLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             HHhCCCHHHHHHHHHHHHhcC-CCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            457899999999999876532 12222    34455666677899999999999988752  111 1  12345556667


Q ss_pred             HHHcCChhHHHHHHHHHHh----CCCC--C-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          187 FLKDGSPADAMNIYEDMIK----SPDP--P-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       187 ~~~~g~~~~a~~~~~~M~~----~g~~--p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +...|++++|.+.+++..+    .|..  | ....+..+-..+...|++++|..
T Consensus       541 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~  594 (903)
T PRK04841        541 LFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQ  594 (903)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            7889999999999987654    2321  1 22334455566777899999877

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

Probab=86.06  E-value=6.5  Score=26.86  Aligned_cols=76  Identities=13%  Similarity=0.090  Sum_probs=49.5

Q ss_pred             HHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHH
Q 025225          145 YKDLIIALARTG--KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKG  221 (256)
Q Consensus       145 y~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~  221 (256)
                      |++--..|....  +.-+..+-++.+-...+.|+.....+.+++|-+.+++.-|.++|+-.+.. +.+....|..+++-
T Consensus        11 F~ary~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lqE   88 (108)
T PF02284_consen   11 FDARYEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQE   88 (108)
T ss_dssp             HHHHHHHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHHH
T ss_pred             HHHHHHHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHHH
Confidence            344333444433  33466777777777789999999999999999999999999999988754 22233378777753

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 ....

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=85.82  E-value=7.4  Score=36.76  Aligned_cols=144  Identities=13%  Similarity=0.024  Sum_probs=79.4

Q ss_pred             cccccccCCchHHHHHHHHHhcCCCccccccccCCCCCCCCcccCcccccccccccCCC-CC---CccccccccchhHHH
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRP-RG---SLWRGKKLIGKEALF   78 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~~~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~-~~---~~~~~~~~~~~~~~~   78 (256)
                      .+.|.-.|..|.|-+-++-++...+|.-+-+-|.+-.+++-+     .-++..|....- +.   ....... ..+.. .
T Consensus       735 FSfyvtiG~MD~AfksI~~IkS~~vW~nmA~McVkT~RLDVA-----kVClGhm~~aRgaRAlR~a~q~~~e-~eakv-A  807 (1416)
T KOG3617|consen  735 FSFYVTIGSMDAAFKSIQFIKSDSVWDNMASMCVKTRRLDVA-----KVCLGHMKNARGARALRRAQQNGEE-DEAKV-A  807 (1416)
T ss_pred             eeEEEEeccHHHHHHHHHHHhhhHHHHHHHHHhhhhccccHH-----HHhhhhhhhhhhHHHHHHHHhCCcc-hhhHH-H
Confidence            356778899999999999888888899999999988888776     555555543221 10   0000000 01111 1


Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHH-HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELE-RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~-~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      ++  ....|-.++|. .+++..++       +.|++-+. ..|.+++|+++-+.=-+.    .-..||-.--.-+-..++
T Consensus       808 vL--AieLgMlEeA~-~lYr~ckR-------~DLlNKlyQs~g~w~eA~eiAE~~DRi----HLr~Tyy~yA~~Lear~D  873 (1416)
T KOG3617|consen  808 VL--AIELGMLEEAL-ILYRQCKR-------YDLLNKLYQSQGMWSEAFEIAETKDRI----HLRNTYYNYAKYLEARRD  873 (1416)
T ss_pred             HH--HHHHhhHHHHH-HHHHHHHH-------HHHHHHHHHhcccHHHHHHHHhhccce----ehhhhHHHHHHHHHhhcc
Confidence            11  13455566665 34333322       13444443 467788887776542222    233344444444455566


Q ss_pred             HHHHHHHHHH
Q 025225          158 MNEAMQVWES  167 (256)
Q Consensus       158 ~~~a~~~~~~  167 (256)
                      .+.|.+.|++
T Consensus       874 i~~AleyyEK  883 (1416)
T KOG3617|consen  874 IEAALEYYEK  883 (1416)
T ss_pred             HHHHHHHHHh
Confidence            6666666654

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

Probab=85.82  E-value=18  Score=29.71  Aligned_cols=91  Identities=12%  Similarity=0.085  Sum_probs=55.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCHhhHHHHHHHHHH--cC-ChhHHHHHHHHHHhCCCCC-Chh
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKE-DLFPDSQTYTEVIRGFLK--DG-SPADAMNIYEDMIKSPDPP-EEL  213 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~--~g-~~~~a~~~~~~M~~~g~~p-~~~  213 (256)
                      .-|...|--|=..|...|+++.|..-|.+-.+. |=.|  ..+..+-.++..  .+ +..++.++|++....  .| |..
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~--~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~--D~~~ir  228 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNP--EILLGLAEALYYQAGQQMTAKARALLRQALAL--DPANIR  228 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCH--HHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc--CCccHH
Confidence            457777777777788888888887777776663 3323  333333333222  22 345677777777654  22 334


Q ss_pred             HHHHHHHHhcCCCChHHHHH
Q 025225          214 PFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       214 t~~~li~~~~~~g~~~~a~~  233 (256)
                      .-..|-..+...|++.+|+.
T Consensus       229 al~lLA~~afe~g~~~~A~~  248 (287)
T COG4235         229 ALSLLAFAAFEQGDYAEAAA  248 (287)
T ss_pred             HHHHHHHHHHHcccHHHHHH
Confidence            44455567777777777766

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=85.45  E-value=8.8  Score=25.94  Aligned_cols=64  Identities=16%  Similarity=0.133  Sum_probs=50.7

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKG  221 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~  221 (256)
                      +.-++.+-++.+....+.|+.....+-+++|-+.+++.-|.++|+-.+.. +..+...|..++.-
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~lqe   85 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYILQE   85 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHHHH
Confidence            55677777888888889999999999999999999999999999987743 11245577777653

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.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=85.37  E-value=2.3  Score=22.98  Aligned_cols=29  Identities=10%  Similarity=0.381  Sum_probs=23.7

Q ss_pred             HhhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          177 SQTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       177 ~~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      ..+++.|-..|...|++++|..++++..+
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            45788899999999999999999988764

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=85.10  E-value=20  Score=29.43  Aligned_cols=57  Identities=7%  Similarity=-0.045  Sum_probs=23.0

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      |.+++..+++.+++...-+--+.. -+.-.....-.|-.|.|.++...+.++-....+
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~p-EklPpkIleLCILLysKv~Ep~amlev~~~WL~  146 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVP-EKLPPKILELCILLYSKVQEPAAMLEVASAWLQ  146 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCc-ccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            444444444444443332222221 122233333344444444444444444444443

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>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=84.84  E-value=12  Score=29.02  Aligned_cols=79  Identities=9%  Similarity=0.085  Sum_probs=51.0

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC---CCCCChhHHHHHHHHhcCCCCh
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS---PDPPEELPFRILLKGLLPHPLL  228 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~---g~~p~~~t~~~li~~~~~~g~~  228 (256)
                      +.+.|+ ++|.+.|-++...+.--|...--.|-.-| -..+.+++..++.+..+.   +-.+|+..+.+|...|-+.|++
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY-~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~  194 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYY-TKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNY  194 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcch
Confidence            455555 55666677766665544444444444444 367778888888776643   3467788888888888888877


Q ss_pred             HHHH
Q 025225          229 RSKV  232 (256)
Q Consensus       229 ~~a~  232 (256)
                      +.|.
T Consensus       195 e~AY  198 (203)
T PF11207_consen  195 EQAY  198 (203)
T ss_pred             hhhh
Confidence            7663

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=84.61  E-value=17  Score=28.18  Aligned_cols=146  Identities=18%  Similarity=0.190  Sum_probs=82.2

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhc-cCCC---cHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLR-LLKM---DIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~-~~~~---~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      -..+...|+..+|+..| +..... .-.|   +.. .+..++-+.|++++|...++++.+..+-.| ..-+-..+.+.+.
T Consensus        12 a~~~~~~g~y~~Ai~~f-~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~-~~~~A~Y~~g~~~   89 (203)
T PF13525_consen   12 ALEALQQGDYEEAIKLF-EKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSP-KADYALYMLGLSY   89 (203)
T ss_dssp             HHHHHHCT-HHHHHHHH-HHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-T-THHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHH-HHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc-chhhHHHHHHHHH
Confidence            34567889999998655 444433 2222   222 488899999999999999999888752223 2334444444432


Q ss_pred             c-------------CCHHHHHHHHHHHHhCCCCCCHh------hH------------HHHHHHHHHcCChhHHHHHHHHH
Q 025225          155 T-------------GKMNEAMQVWESMRKEDLFPDSQ------TY------------TEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       155 ~-------------g~~~~a~~~~~~m~~~g~~p~~~------t~------------~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      .             +...+|...|+++.+.  -|++.      ..            -.+-.-|.+.|.+.-|..-++.+
T Consensus        90 ~~~~~~~~~~~~D~~~~~~A~~~~~~li~~--yP~S~y~~~A~~~l~~l~~~la~~e~~ia~~Y~~~~~y~aA~~r~~~v  167 (203)
T PF13525_consen   90 YKQIPGILRSDRDQTSTRKAIEEFEELIKR--YPNSEYAEEAKKRLAELRNRLAEHELYIARFYYKRGKYKAAIIRFQYV  167 (203)
T ss_dssp             HHHHHHHH-TT---HHHHHHHHHHHHHHHH---TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHH
T ss_pred             HHhCccchhcccChHHHHHHHHHHHHHHHH--CcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            2             2245666667666642  13321      11            12334467777777787777777


Q ss_pred             HhC--CCCCChhHHHHHHHHhcCCCChH
Q 025225          204 IKS--PDPPEELPFRILLKGLLPHPLLR  229 (256)
Q Consensus       204 ~~~--g~~p~~~t~~~li~~~~~~g~~~  229 (256)
                      .+.  +-.-.....-.++++|.+.|..+
T Consensus       168 ~~~yp~t~~~~~al~~l~~~y~~l~~~~  195 (203)
T PF13525_consen  168 IENYPDTPAAEEALARLAEAYYKLGLKQ  195 (203)
T ss_dssp             HHHSTTSHHHHHHHHHHHHHHHHTT-HH
T ss_pred             HHHCCCCchHHHHHHHHHHHHHHhCChH
Confidence            765  22222233456777777777655

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=84.45  E-value=18  Score=30.99  Aligned_cols=100  Identities=11%  Similarity=0.126  Sum_probs=53.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC-CCC-C-CHhhHHHHHHHHHH---cCChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          147 DLIIALARTGKMNEAMQVWESMRKE-DLF-P-DSQTYTEVIRGFLK---DGSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       147 ~li~~~~~~g~~~~a~~~~~~m~~~-g~~-p-~~~t~~~li~~~~~---~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      .++-+|-...+++...++.+.|... .+. + +...=-...-++-+   .|+.++|.+++.......-.+++.||..+-+
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            3344577777777777777777763 110 1 11111122223334   5777777777777666555666667766555


Q ss_pred             HhcC---------CCChHHHHHhhhhhcCCCcccc
Q 025225          221 GLLP---------HPLLRSKVKKDFEELFPEKHAY  246 (256)
Q Consensus       221 ~~~~---------~g~~~~a~~~~~~~~~p~~~~~  246 (256)
                      .|-.         ...+++|+..-.++++-+...|
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~~~~Y  260 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYRKGFEIEPDYY  260 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHHHHHcCCcccc
Confidence            4321         1234555554445555553333

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

Probab=84.22  E-value=3.6  Score=21.18  Aligned_cols=27  Identities=22%  Similarity=0.313  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      +|..+-..|...|++++|...|++..+
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            455555555666666666666665544

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 ....

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

Probab=83.88  E-value=28  Score=30.29  Aligned_cols=126  Identities=14%  Similarity=0.018  Sum_probs=84.4

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHH---HcCCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELE---RQEETILAVKIFDIIRKQDWYQPD-AYIYKDLIIA  151 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~---~~~~~~~a~~~~~~m~~~~~~~p~-~~~y~~li~~  151 (256)
                      |--+++.|...++.++|.-..-..+..-+-.....+|+.+.+   ...--++|..+++.-.+..   |+ +..-+.+-..
T Consensus       371 Y~GL~hsYLA~~~~kEA~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~---P~Y~~AV~~~AEL  447 (564)
T KOG1174|consen  371 YRGLFHSYLAQKRFKEANALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKIN---PIYTPAVNLIAEL  447 (564)
T ss_pred             HHHHHHHHHhhchHHHHHHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccC---CccHHHHHHHHHH
Confidence            334578888888888886322222222111111124553222   2234588988888766553   44 3445566677


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      +...|..+++..+++.-..  ..||...-+.|-+-+...+.+++|++.|..-...
T Consensus       448 ~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~  500 (564)
T KOG1174|consen  448 CQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQ  500 (564)
T ss_pred             HHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            7788999999999998776  4689999999999999999999999988765544

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

Probab=83.82  E-value=37  Score=31.51  Aligned_cols=135  Identities=15%  Similarity=0.109  Sum_probs=90.5

Q ss_pred             cCCCcHHHHHHHHHHHhhccCCCcHHH----HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHH
Q 025225           85 RFKDDEEKLQKFIKTHVLRLLKMDIVA----VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNE  160 (256)
Q Consensus        85 ~~~~~~~a~~~~~~~~~~~~~~~~~~~----li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~  160 (256)
                      -.++.++|+ .++.+..+.  -|+...    +=..+-+.++.+.|...|..-.+.  |...+..|-.|-..=-+.|.+-+
T Consensus       663 ~ld~~eeA~-rllEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~--cP~~ipLWllLakleEk~~~~~r  737 (913)
T KOG0495|consen  663 YLDNVEEAL-RLLEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK--CPNSIPLWLLLAKLEEKDGQLVR  737 (913)
T ss_pred             HhhhHHHHH-HHHHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc--CCCCchHHHHHHHHHHHhcchhh
Confidence            456666776 333333221  244442    333455667778888877765555  56677788888888888899999


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCC
Q 025225          161 AMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHP  226 (256)
Q Consensus       161 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g  226 (256)
                      |..+|+.-+-.+ +-|...|-..|+.=.+.|+.+.|..++.+..+. +.-+...|.--|....+.+
T Consensus       738 AR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~  801 (913)
T KOG0495|consen  738 ARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQ  801 (913)
T ss_pred             HHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcc
Confidence            999999877654 237789999999999999999999988877664 3333444444444444443

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=83.75  E-value=4.8  Score=23.21  Aligned_cols=32  Identities=6%  Similarity=0.091  Sum_probs=22.6

Q ss_pred             HcCChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          189 KDGSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       189 ~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      +.|-.+++..++++|.+.|+..+...|..+++
T Consensus        14 ~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen   14 RRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            55666677777777777777777777766665

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>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=82.97  E-value=18  Score=27.24  Aligned_cols=118  Identities=14%  Similarity=0.184  Sum_probs=74.1

Q ss_pred             HHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHH
Q 025225           93 LQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG--KMNEAMQVWES  167 (256)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g--~~~~a~~~~~~  167 (256)
                      +-++.+.....++.|+..   -+|+.+.+.|++..-    ..+.+.+ +.+|...-...+-.+....  -..-|.+++.+
T Consensus        13 llEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L----~qllq~~-Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   13 LLEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQL----HQLLQYH-VIPDSKPLACQLLSLGNQYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHH----HHHHhhc-ccCCcHHHHHHHHHhHccChHHHHHHHHHHHH
Confidence            345666667777777654   388888888886655    4455555 6777777776665555432  23444444444


Q ss_pred             HHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCC
Q 025225          168 MRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPL  227 (256)
Q Consensus       168 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~  227 (256)
                      +..        .+..+++.+...|++-+|.++.+.....    +...-..++++-.+.++
T Consensus        88 L~~--------~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D  135 (167)
T PF07035_consen   88 LGT--------AYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSND  135 (167)
T ss_pred             hhh--------hHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCC
Confidence            442        3567778888889998888888775332    22333556666666654

>PRK11906 transcriptional regulator; Provisional

Probab=82.96  E-value=33  Score=30.28  Aligned_cols=111  Identities=13%  Similarity=0.214  Sum_probs=80.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH---hhHHHHHHHHHHcCChhHH
Q 025225          120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS---QTYTEVIRGFLKDGSPADA  196 (256)
Q Consensus       120 ~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~---~t~~~li~~~~~~g~~~~a  196 (256)
                      .+..+|.+.-..-.+.+  .-|......+=.+....++++.|..+|++....  .||.   ..|..++..+  +|+.++|
T Consensus       318 ~~~~~a~~~A~rAveld--~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L--~Pn~A~~~~~~~~~~~~--~G~~~~a  391 (458)
T PRK11906        318 LAAQKALELLDYVSDIT--TVDGKILAIMGLITGLSGQAKVSHILFEQAKIH--STDIASLYYYRALVHFH--NEKIEEA  391 (458)
T ss_pred             HHHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhc--CCccHHHHHHHHHHHHH--cCCHHHH
Confidence            35678888888888887  678888877777778888899999999997763  4653   4455555554  7999999


Q ss_pred             HHHHHHHHh-CCCCCChhHHHHHHHHhcCCCChHHHHHhhhh
Q 025225          197 MNIYEDMIK-SPDPPEELPFRILLKGLLPHPLLRSKVKKDFE  237 (256)
Q Consensus       197 ~~~~~~M~~-~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  237 (256)
                      .+.+++-.+ +-.+--....--.|+.|+.++. +++++.-.+
T Consensus       392 ~~~i~~alrLsP~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  432 (458)
T PRK11906        392 RICIDKSLQLEPRRRKAVVIKECVDMYVPNPL-KNNIKLYYK  432 (458)
T ss_pred             HHHHHHHhccCchhhHHHHHHHHHHHHcCCch-hhhHHHHhh
Confidence            999998444 3334444555566778887764 778774433

>PLN02789 farnesyltranstransferase

Probab=82.72  E-value=28  Score=29.28  Aligned_cols=138  Identities=12%  Similarity=0.056  Sum_probs=85.5

Q ss_pred             HhhcCC-CcHHHHHHHHHHHhhccCCCcHH-H---HHHHHHHcCC--HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           82 GLKRFK-DDEEKLQKFIKTHVLRLLKMDIV-A---VLIELERQEE--TILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        82 ~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~-~---li~~~~~~~~--~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      .+...+ ..++++ .+++...+..  |... +   --..+.+.|.  .++++.+++.+.+..  .-|..+|+-.--.+.+
T Consensus        80 iL~~L~~~l~eeL-~~~~~~i~~n--pknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~d--pkNy~AW~~R~w~l~~  154 (320)
T PLN02789         80 CLEALDADLEEEL-DFAEDVAEDN--PKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLD--AKNYHAWSHRQWVLRT  154 (320)
T ss_pred             HHHHcchhHHHHH-HHHHHHHHHC--CcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhC--cccHHHHHHHHHHHHH
Confidence            334445 456776 4445554433  3322 1   1111233444  377899999999886  6789999999999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC---ChhHHHH-HHHHH-HhCCCC-CChhHHHHHHHHhcCC
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG---SPADAMN-IYEDM-IKSPDP-PEELPFRILLKGLLPH  225 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g---~~~~a~~-~~~~M-~~~g~~-p~~~t~~~li~~~~~~  225 (256)
                      .|+++++.+.++++.+.+. -|...|+...-.+.+.|   ..+...+ -+.-- ...... -|...|+.+-..|...
T Consensus       155 l~~~~eeL~~~~~~I~~d~-~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~  230 (320)
T PLN02789        155 LGGWEDELEYCHQLLEEDV-RNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDD  230 (320)
T ss_pred             hhhHHHHHHHHHHHHHHCC-CchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcC
Confidence            9999999999999998654 36677777666665553   3322111 11111 122333 4677888777777763

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=81.94  E-value=28  Score=28.78  Aligned_cols=89  Identities=13%  Similarity=0.086  Sum_probs=37.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      +..+|...|+++.|..+++.+...- -......-..-|..+.+.....+...+-.+.-..   | |...=-.+-..|...
T Consensus       174 la~~~l~~g~~e~A~~iL~~lP~~~-~~~~~~~l~a~i~ll~qaa~~~~~~~l~~~~aad---Pdd~~aa~~lA~~~~~~  249 (304)
T COG3118         174 LAECLLAAGDVEAAQAILAALPLQA-QDKAAHGLQAQIELLEQAAATPEIQDLQRRLAAD---PDDVEAALALADQLHLV  249 (304)
T ss_pred             HHHHHHHcCChHHHHHHHHhCcccc-hhhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhC---CCCHHHHHHHHHHHHHc
Confidence            5555555555555555555554332 1111112122233333333333333333332221   3 333333444445555


Q ss_pred             CChhHHHHHHHHHH
Q 025225          191 GSPADAMNIYEDMI  204 (256)
Q Consensus       191 g~~~~a~~~~~~M~  204 (256)
                      |+.+.|.+.+-.+.
T Consensus       250 g~~e~Ale~Ll~~l  263 (304)
T COG3118         250 GRNEAALEHLLALL  263 (304)
T ss_pred             CCHHHHHHHHHHHH
Confidence            66666555554444

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=81.89  E-value=33  Score=29.58  Aligned_cols=121  Identities=12%  Similarity=0.053  Sum_probs=78.9

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhh----ccCCCcHH------------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVL----RLLKMDIV------------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYI  144 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~------------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~  144 (256)
                      +.|.+.|++..|...+-+...-    .+..+.-.            .+--++.+.+++.+|++.=+.....+  .+|+-.
T Consensus       216 n~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~--~~N~KA  293 (397)
T KOG0543|consen  216 NVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD--PNNVKA  293 (397)
T ss_pred             hHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC--CCchhH
Confidence            3667888888887554321111    11111110            25556678889999999888888776  667665


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH-cCC-hhHHHHHHHHHHh
Q 025225          145 YKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK-DGS-PADAMNIYEDMIK  205 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~-~g~-~~~a~~~~~~M~~  205 (256)
                      .=--=.+|...|+++.|...|+++.+  +.|+-..-+.=|..|.+ ..+ .++..++|..|..
T Consensus       294 LyRrG~A~l~~~e~~~A~~df~ka~k--~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  294 LYRRGQALLALGEYDLARDDFQKALK--LEPSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            55556677788999999999999888  46766655555555544 333 3455778888864

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=81.86  E-value=18  Score=29.67  Aligned_cols=86  Identities=13%  Similarity=0.093  Sum_probs=65.7

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhh-ccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc-
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVL-RLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART-  155 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~-  155 (256)
                      -|.+++..+++.+.+.-+++.... ..++|.+. -.|-.|.|.+++..+.++-....+.. -.-+...|.++...|..+ 
T Consensus        89 GIQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p-~Nq~lp~y~~vaELyLl~V  167 (309)
T PF07163_consen   89 GIQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDP-SNQSLPEYGTVAELYLLHV  167 (309)
T ss_pred             hHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCc-ccCCchhhHHHHHHHHHHH
Confidence            388999999999988655554443 23444444 36888999999999999999776654 355666699999998875 


Q ss_pred             ----CCHHHHHHHH
Q 025225          156 ----GKMNEAMQVW  165 (256)
Q Consensus       156 ----g~~~~a~~~~  165 (256)
                          |.+++|+++.
T Consensus       168 LlPLG~~~eAeelv  181 (309)
T PF07163_consen  168 LLPLGHFSEAEELV  181 (309)
T ss_pred             HhccccHHHHHHHH
Confidence                9999999887

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>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=81.77  E-value=16  Score=27.72  Aligned_cols=61  Identities=20%  Similarity=0.192  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      .+..+-..|++.|+.++|.+.|.++.+....|.  ...+-.+|+.....|++..+.....+..
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            344555555555555555555555555433332  2334455555555555555555554443

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.

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=81.21  E-value=8.9  Score=29.40  Aligned_cols=53  Identities=21%  Similarity=0.246  Sum_probs=32.0

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      ...+.+......+...+.-+..|++.+|..++.++...|+.++|.++.+++..
T Consensus       120 ~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~  172 (193)
T PF11846_consen  120 LPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARARR  172 (193)
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44444444444444433322467777777777777777777777777777665

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=80.95  E-value=50  Score=31.03  Aligned_cols=113  Identities=18%  Similarity=0.092  Sum_probs=51.0

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChh
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPA  194 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~  194 (256)
                      +.+.+..++|...+.+..+..  ......|.-.=..+...|..++|.+.|..-..  +.|| +.+.+++-..+.+.|+..
T Consensus       660 ~~~~~~~~~a~~CL~Ea~~~~--~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~--ldP~hv~s~~Ala~~lle~G~~~  735 (799)
T KOG4162|consen  660 FLLSGNDDEARSCLLEASKID--PLSASVYYLRGLLLEVKGQLEEAKEAFLVALA--LDPDHVPSMTALAELLLELGSPR  735 (799)
T ss_pred             HHhcCCchHHHHHHHHHHhcc--hhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHh--cCCCCcHHHHHHHHHHHHhCCcc
Confidence            344444455544444444432  33333444433444444555555555544333  2232 344444555555555444


Q ss_pred             HHHH--HHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          195 DAMN--IYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       195 ~a~~--~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      -|..  ++.++.+.+. -+...|-.+=..+-+.|+.++|.+
T Consensus       736 la~~~~~L~dalr~dp-~n~eaW~~LG~v~k~~Gd~~~Aae  775 (799)
T KOG4162|consen  736 LAEKRSLLSDALRLDP-LNHEAWYYLGEVFKKLGDSKQAAE  775 (799)
T ss_pred             hHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHccchHHHHH
Confidence            4444  4555444421 233444445555555555555544

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

Probab=80.83  E-value=44  Score=30.40  Aligned_cols=122  Identities=15%  Similarity=0.078  Sum_probs=74.0

Q ss_pred             HHHHhhcCCCcHHHHHHHHH--------HHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcC-CCCCCHHHHHHH
Q 025225           79 VILGLKRFKDDEEKLQKFIK--------THVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQD-WYQPDAYIYKDL  148 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~--------~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~-~~~p~~~~y~~l  148 (256)
                      .+.-....|+++.|+..+ .        ...+.+..|.++ +++..+.+.++-+.|-.++++-.+.= .-.+.....+++
T Consensus       382 ~aQl~is~gn~~~A~~il-~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~  460 (652)
T KOG2376|consen  382 RAQLKISQGNPEVALEIL-SLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSL  460 (652)
T ss_pred             HHHHHHhcCCHHHHHHHH-HHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhH
Confidence            345556778888887433 4        344555667666 46666666666666666666543220 002222333333


Q ss_pred             H----HHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          149 I----IALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       149 i----~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      +    ..-.+.|.-++|.++++++.+.+ .+|..+...++.+|++. ++++|..+-..+
T Consensus       461 ~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~-d~eka~~l~k~L  517 (652)
T KOG2376|consen  461 MREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL-DPEKAESLSKKL  517 (652)
T ss_pred             HHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc-CHHHHHHHhhcC
Confidence            3    33346688888888888887732 36788888888888864 466777665544

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=80.53  E-value=1.9  Score=30.99  Aligned_cols=28  Identities=21%  Similarity=0.462  Sum_probs=13.5

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 025225          156 GKMNEAMQVWESMRKEDLFPDSQTYTEVIR  185 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  185 (256)
                      |.-.+|..+|.+|.++|-.||  .|+.|+.
T Consensus       109 gsk~DaY~VF~kML~~G~pPd--dW~~Ll~  136 (140)
T PF11663_consen  109 GSKTDAYAVFRKMLERGNPPD--DWDALLK  136 (140)
T ss_pred             ccCCcHHHHHHHHHhCCCCCc--cHHHHHH
Confidence            334445555555555555444  3444443

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.50  E-value=11  Score=35.07  Aligned_cols=120  Identities=10%  Similarity=0.050  Sum_probs=87.5

Q ss_pred             ccCCCcHHHHHHHHHHcCCHHH----------HHHHHHHHHhc-CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          103 RLLKMDIVAVLIELERQEETIL----------AVKIFDIIRKQ-DWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       103 ~~~~~~~~~li~~~~~~~~~~~----------a~~~~~~m~~~-~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      .+..|+..+.=++|.+.....-          -++++..+..+ | ....--+-+--+.-+..-|.-.+|.++-.+.+- 
T Consensus       635 ~~r~~~lk~~a~~~a~sk~~s~e~ka~ed~~kLl~lQ~~Le~q~~-~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fki-  712 (829)
T KOG2280|consen  635 EGRIPALKTAANAFAKSKEKSFEAKALEDQMKLLKLQRTLEDQFG-GSFVDLSLHDTVTTLILIGQNKRAEQLKSDFKI-  712 (829)
T ss_pred             cccchhHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhc-cccccCcHHHHHHHHHHccchHHHHHHHHhcCC-
Confidence            4566777667777776655221          12222333322 3 344555667777888889999999999888876 


Q ss_pred             CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          172 DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       172 g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                         ||-.-|--=+.+++..+++++-+++-..++.      +.-|.-.++.|.+.|+.+||.+
T Consensus       713 ---pdKr~~wLk~~aLa~~~kweeLekfAkskks------PIGy~PFVe~c~~~~n~~EA~K  765 (829)
T KOG2280|consen  713 ---PDKRLWWLKLTALADIKKWEELEKFAKSKKS------PIGYLPFVEACLKQGNKDEAKK  765 (829)
T ss_pred             ---cchhhHHHHHHHHHhhhhHHHHHHHHhccCC------CCCchhHHHHHHhcccHHHHhh
Confidence               9999999999999999999888877766553      4556668899999999999988

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	256
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 46.7 bits (109), Expect = 4e-06
 Identities = 20/117 (17%), Positives = 38/117 (32%), Gaps = 6/117 (5%)

Query: 140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNI 199
               +Y  +++  AR G   E + V   ++   L PD  +Y   ++   +    A  +  
Sbjct: 163 LTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIER 222

Query: 200 Y-EDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPEKHAYDPPEEIFGK 255
             E M +     + L   +LL         R+ V K   ++ P              
Sbjct: 223 CLEQMSQEGLKLQALFTAVLLS-----EEDRATVLKAVHKVKPTFSLPPQLPPPVNT 274

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 5e-05
 Identities = 44/259 (16%), Positives = 82/259 (31%), Gaps = 61/259 (23%)

Query: 12  PILASIVLQNLTKNPS--KNFSFLAFKPKSPIVD-FVAH-EPILGLRQYHDGRPRGSLWR 67
           P   SI+ +++    +   N+  +     + I++  +   EP    + +       S++ 
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL----SVFP 382

Query: 68  GKKLIGKEALFVIL-GLKRFKDDEEKLQKFIKTHVLRLLKMD-------IVAVLIELERQ 119
               I    L  ++       D    + K  K     L++         I ++ +EL+ +
Sbjct: 383 PSAHI-PTILLSLIWFDVIKSDVMVVVNKLHK---YSLVEKQPKESTISIPSIYLELKVK 438

Query: 120 EETILAV--KIFD---IIRKQDWYQP-----DAYIYKDLIIALARTGKMNEAMQVWESMR 169
            E   A+   I D   I +  D         D Y Y  +   L             E   
Sbjct: 439 LENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI----------EHPE 488

Query: 170 KEDLFPDSQTYTEVIRGFLK-----DGSPADA----------MNIYEDMIKSPDPPEELP 214
           +  LF     + +    FL+     D +  +A          +  Y+  I   DP  E  
Sbjct: 489 RMTLFR--MVFLDF--RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL 544

Query: 215 FRILLKGLLPHP--LLRSK 231
              +L  L      L+ SK
Sbjct: 545 VNAILDFLPKIEENLICSK 563

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 4e-04
 Identities = 45/297 (15%), Positives = 83/297 (27%), Gaps = 80/297 (26%)

Query: 6   FSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRP-RGS 64
                 P     +LQ L      N++  +    +  +    H     LR+    +P    
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI--HSIQAELRRLLKSKPYENC 246

Query: 65  L------WRGKKLIGKEALFV---ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIE 115
           L         K      A  +   IL   RFK   + L     TH+       +    + 
Sbjct: 247 LLVLLNVQNAKAW---NAFNLSCKILLTTRFKQVTDFLSAATTTHI------SLDHHSMT 297

Query: 116 LERQE-ETILA----VKIFDIIRKQDWYQPDAYIYKDLIIAL--ARTGKMNEAMQVWESM 168
           L   E +++L      +  D+ R+     P         +++              W+ +
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNP-------RRLSIIAESIRDGLATWDNWKHV 350

Query: 169 RKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDM------IKSP---------DPPEEL 213
             + L       T +I   L    PA+   +++ +         P         D  +  
Sbjct: 351 NCDKL-------TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403

Query: 214 PFRIL----LKGL-----------LPHPLLRSKVKKDFEELFPEKH-----AYDPPE 250
              ++       L           +P   L  KVK + E      H      Y+ P+
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE---YALHRSIVDHYNIPK 457

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	256
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.93
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.9
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.79
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.76
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.48
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.43
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.35
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.34
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.31
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.25
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.25
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.23
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.2
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.19
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.14
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.11
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.11
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.1
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.09
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.08
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.07
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.07
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.06
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.03
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.03
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.03
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.02
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.0
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.97
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.96
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.95
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.93
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.92
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.91
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.86
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.85
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.85
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.84
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.81
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.8
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.74
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.73
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.71
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.66
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.58
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.56
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.56
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.53
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.52
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.52
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.49
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.48
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.48
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.47
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.46
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.45
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.45
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.37
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.3
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.27
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.26
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.24
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.24
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.24
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.23
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.23
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.23
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.21
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.2
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.19
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.19
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.19
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.17
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.17
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.15
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.15
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.13
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.12
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.12
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.09
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.08
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.07
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.07
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.06
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.06
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.05
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.05
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.04
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.04
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.02
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.0
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.0
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.99
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.99
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.97
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.97
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.96
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.96
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.95
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.95
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.94
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.93
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.92
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.92
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.92
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.9
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.87
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.86
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.84
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.83
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.82
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.81
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.81
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.8
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.79
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.78
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.77
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.75
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.75
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.75
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.73
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.73
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.72
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.72
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.71
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.69
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.68
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.64
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.63
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.62
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.6
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.59
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.58
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.56
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.56
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.55
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.54
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.54
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.54
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.52
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.51
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.5
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.5
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.5
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.48
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.46
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.45
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.45
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.43
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.42
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.4
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.4
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.38
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.38
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.37
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.36
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.36
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.36
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.36
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.35
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.3
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.26
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.25
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.25
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.23
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.22
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.22
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.14
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.13
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.08
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.01
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.94
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.87
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.84
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.83
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.8
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.75
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.72
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.69
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.6
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.58
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.55
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.54
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.54
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	96.52
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.47
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.46
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.45
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.42
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.37
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.36
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.32
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.29
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.27
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.26
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.26
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	95.98
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.66
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	95.62
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.45
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	95.32
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.05
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	94.56
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	94.54
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	94.42
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	94.26
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	94.17
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	93.33
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	93.14
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	93.1
2p58_C	116	Putative type III secretion protein YSCG; type III	92.92
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.87
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.51
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	92.5
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.48
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	92.48
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	92.28
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.07
1pc2_A	152	Mitochondria fission protein; unknown function; NM	91.68
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	90.99
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	90.96
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	90.27
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	89.84
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	89.75
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	89.28
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	88.79
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	88.4
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	87.4
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	87.39
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.62
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	85.09
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	84.14
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	83.86
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	83.67
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	83.57
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	81.23

>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=100.00  E-value=4.1e-36  Score=263.06  Aligned_cols=179  Identities=17%  Similarity=0.125  Sum_probs=169.1

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCC---------HHHHHHHHHHHHhcCCCCCCH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEE---------TILAVKIFDIIRKQDWYQPDA  142 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~---------~~~a~~~~~~m~~~~~~~p~~  142 (256)
                      .+...|.+||+.|+.++|+ .++++|.+.|++||..   +||.+|++.+.         +++|.++|++|.+.| +.||.
T Consensus        28 ~l~~~id~c~k~G~~~~A~-~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G-~~Pd~  105 (501)
T 4g26_A           28 LLKQKLDMCSKKGDVLEAL-RLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDK-VVPNE  105 (501)
T ss_dssp             HHHHHHHHTTTSCCHHHHH-HHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTT-CCCCH
T ss_pred             HHHHHHHHHHhCCCHHHHH-HHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhC-CCCCH
Confidence            3556799999999999998 6778999999999987   59999987654         799999999999999 99999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      +|||+||.+|++.|++++|.++|++|.+.|+.||..|||+||.+||+.|++++|.++|++|.+.|+.||..||++||++|
T Consensus       106 ~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~  185 (501)
T 4g26_A          106 ATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVS  185 (501)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCChHHHHH----hhhhhcCCCcccccchhHhhcc
Q 025225          223 LPHPLLRSKVK----KDFEELFPEKHAYDPPEEIFGK  255 (256)
Q Consensus       223 ~~~g~~~~a~~----~~~~~~~p~~~~~~~li~~y~~  255 (256)
                      ++.|++++|.+    |...+..|+..||+++++.|.+
T Consensus       186 ~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          186 MDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             hhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            99999999988    8889999999999999998864

>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=100.00  E-value=9.4e-35  Score=254.45  Aligned_cols=198  Identities=8%  Similarity=0.080  Sum_probs=169.2

Q ss_pred             hHHHHHHHHHhcCCC-------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhc
Q 025225           13 ILASIVLQNLTKNPS-------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKR   85 (256)
Q Consensus        13 ~~A~~l~~~m~~~~~-------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~   85 (256)
                      ..+..+.+.+++.++       ++.+|.+|++.|++..+     +++|++|...+..|+..+|+.        +|.+|++
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A-----~~lf~~M~~~Gv~pd~~tyn~--------Li~~c~~   73 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEA-----LRLYDEARRNGVQLSQYHYNV--------LLYVCSL   73 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTSCCHHHH-----HHHHHHHHHHTCCCCHHHHHH--------HHHHHTT
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHH-----HHHHHHHHHcCCCCCHhHHHH--------HHHHHHh
Confidence            345566677766554       78889999999999999     999999999998886555554        4788887


Q ss_pred             CCC---------cHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           86 FKD---------DEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        86 ~~~---------~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+.         .++|. .++++|...|+.||..   +||++|++.|++++|+++|++|.+.| +.||..|||++|.+|+
T Consensus        74 ~~~~~~~~~~~~l~~A~-~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g-~~Pd~~tyn~lI~~~~  151 (501)
T 4g26_A           74 AEAATESSPNPGLSRGF-DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFG-IQPRLRSYGPALFGFC  151 (501)
T ss_dssp             CCCCSSSSCCHHHHHHH-HHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-CCCCHHHHHHHHHHHH
T ss_pred             CCchhhhhhcchHHHHH-HHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCCccceehHHHHHHH
Confidence            665         46676 6778999999999987   59999999999999999999999999 9999999999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                      +.|++++|.++|++|.+.|+.||..||++||.+|++.|++++|.++|++|++.|+.|+..||++++..|+..
T Consensus       152 ~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          152 RKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999874

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.93  E-value=2.9e-26  Score=208.57  Aligned_cols=142  Identities=15%  Similarity=0.148  Sum_probs=125.6

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh---cCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRK---QDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGF  187 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~---~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  187 (256)
                      ++|++||+.|++++|.++|++|.+   .| +.||++|||+||++||+.|++++|.++|++|.+.|+.||++|||+||.+|
T Consensus       132 aLIdglcK~G~leeA~~Lf~eM~~m~~kG-~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI~gl  210 (1134)
T 3spa_A          132 AFFKCCLLTDQLPLAHHLLVVHHGQRQKR-KLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCM  210 (1134)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHSHHHH-TTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHHhhcC-CCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Confidence            799999999999999999988764   57 89999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCh-hHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhhhhcCCC------cccccchhHhhc
Q 025225          188 LKDGSP-ADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEELFPE------KHAYDPPEEIFG  254 (256)
Q Consensus       188 ~~~g~~-~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~p~------~~~~~~li~~y~  254 (256)
                      |+.|+. ++|.++|++|.+.|+.||..||++++.++.+.+-++ +++....++.|+      ..|...|.+.|.
T Consensus       211 cK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~-~Vrkv~P~f~p~~~~~~~~~t~~LL~dl~s  283 (1134)
T 3spa_A          211 GRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLK-AVHKVKPTFSLPPQLPPPVNTSKLLRDVYA  283 (1134)
T ss_dssp             HHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHH-HHGGGCCCCCCCCCCCCCCCCCTTTHHHHC
T ss_pred             HhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHH-HHHHhCcccCCCCCCcccccchHHHHHHHc
Confidence            999985 789999999999999999999999999888876554 444446666665      556666777665

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.90  E-value=2.6e-24  Score=195.80  Aligned_cols=118  Identities=9%  Similarity=0.006  Sum_probs=107.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---CCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhH
Q 025225          138 YQPDAYIYKDLIIALARTGKMNEAMQVWESMRK---EDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELP  214 (256)
Q Consensus       138 ~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t  214 (256)
                      +.--..|||+||++||+.|++++|.++|++|.+   .|+.||++|||+||+|||+.|++++|.++|++|.+.|+.||..|
T Consensus       123 ~~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvT  202 (1134)
T 3spa_A          123 LSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS  202 (1134)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHH
T ss_pred             HHhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHH
Confidence            344567999999999999999999999988874   48999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCh-HHHHH----hhhhhcCCCcccccchhHhhcc
Q 025225          215 FRILLKGLLPHPLL-RSKVK----KDFEELFPEKHAYDPPEEIFGK  255 (256)
Q Consensus       215 ~~~li~~~~~~g~~-~~a~~----~~~~~~~p~~~~~~~li~~y~~  255 (256)
                      ||+||++||+.|+. ++|.+    |..+|+.||.++|+++++.+++
T Consensus       203 YntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR  248 (1134)
T 3spa_A          203 YAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR  248 (1134)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhH
Confidence            99999999999975 55544    9999999999999999887653

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.79  E-value=8e-19  Score=156.10  Aligned_cols=242  Identities=10%  Similarity=-0.072  Sum_probs=158.3

Q ss_pred             cccccccCCchHHHHHHHHHhcCC--C--ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccc---------
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNP--S--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGK---------   69 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~--~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~---------   69 (256)
                      +..|.+.|+.+.|.++|+.+.+.+  .  |+.+...+.+.++.+.+     +..|+++....+.. ...+.         
T Consensus       279 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~~~~~~~~~-~~~~~~l~~~~~~~  352 (597)
T 2xpi_A          279 LNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDV-----LAITTKILEIDPYN-LDVYPLHLASLHES  352 (597)
T ss_dssp             SCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC-CTTHHHHHHHHHHH
T ss_pred             HHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHH-----HHHHHHHHHcCccc-HHHHHHHHHHHHHh
Confidence            556777777777777777765422  1  66667777777776666     77776665433211 11000         


Q ss_pred             -----------------cccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccC-CCcH-HHHHHHHHHcCCHHHHHHHHH
Q 025225           70 -----------------KLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLL-KMDI-VAVLIELERQEETILAVKIFD  130 (256)
Q Consensus        70 -----------------~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~-~~li~~~~~~~~~~~a~~~~~  130 (256)
                                       .-....+..+...|.+.|+.++|.. +++.+.+... .+.. ..++.+|.+.|++++|.++|+
T Consensus       353 g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~-~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  431 (597)
T 2xpi_A          353 GEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARR-YFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYT  431 (597)
T ss_dssp             TCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHH-HHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHH-HHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                             0012344555677788888888874 3344443221 1111 257777888888888888888


Q ss_pred             HHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----
Q 025225          131 IIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----  206 (256)
Q Consensus       131 ~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----  206 (256)
                      ++.+.+  ..+..+|+.+..+|.+.|++++|.++|+++.+.. ..+..+|+.++..|.+.|++++|.++|++|.+.    
T Consensus       432 ~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  508 (597)
T 2xpi_A          432 TAARLF--QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKT  508 (597)
T ss_dssp             HHHHTT--TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHhC--ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhcc
Confidence            887765  5577788888888888888888888888877642 235777888888888888888888888887765    


Q ss_pred             CCCCC--hhHHHHHHHHhcCCCChHHHHHhh--hhhcCC-CcccccchhHhhc
Q 025225          207 PDPPE--ELPFRILLKGLLPHPLLRSKVKKD--FEELFP-EKHAYDPPEEIFG  254 (256)
Q Consensus       207 g~~p~--~~t~~~li~~~~~~g~~~~a~~~~--~~~~~p-~~~~~~~li~~y~  254 (256)
                      +..|+  ..+|..+..+|.+.|++++|.+..  .....| +..+|..+..+|.
T Consensus       509 ~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  561 (597)
T 2xpi_A          509 QSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYL  561 (597)
T ss_dssp             CCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            66777  678888888888888888887722  222334 4567777766664

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.76  E-value=5.5e-18  Score=150.67  Aligned_cols=230  Identities=9%  Similarity=-0.021  Sum_probs=172.5

Q ss_pred             cccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHH
Q 025225            7 SRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVIL   81 (256)
Q Consensus         7 ~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~   81 (256)
                      .+.|+.+.|.++++.+.+...     |+.+...+.+.++.+.+     +..|+++....+..         ...|..++.
T Consensus       350 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l~~  415 (597)
T 2xpi_A          350 HESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEA-----RRYFSKSSTMDPQF---------GPAWIGFAH  415 (597)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHH-----HHHHHHHHHhCCCC---------HHHHHHHHH
Confidence            344444444444444432111     55555566666666666     66666655432211         346677889


Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccC-CCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLL-KMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN  159 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~  159 (256)
                      .|.+.|+.++|+. +++.+...+. .+... .+..+|.+.|++++|.++|+++.+..  ..+..+|+.+...|.+.|+++
T Consensus       416 ~~~~~g~~~~A~~-~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~  492 (597)
T 2xpi_A          416 SFAIEGEHDQAIS-AYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF--QYDPLLLNELGVVAFNKSDMQ  492 (597)
T ss_dssp             HHHHHTCHHHHHH-HHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHcCCHHHHHH-HHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhCCHH
Confidence            9999999999985 4456654432 12222 58999999999999999999999886  668999999999999999999


Q ss_pred             HHHHHHHHHHhC----CCCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          160 EAMQVWESMRKE----DLFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       160 ~a~~~~~~m~~~----g~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +|.++|+++.+.    +..|+  ..+|+.+...|.+.|++++|.++|+++.+.+ ..+..+|..+..+|.+.|++++|.+
T Consensus       493 ~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~  571 (597)
T 2xpi_A          493 TAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIALVYLHKKIPGLAIT  571 (597)
T ss_dssp             HHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHH
Confidence            999999999875    77888  7899999999999999999999999998775 3478999999999999999999998


Q ss_pred             --hhhhhcCCC-cccccchhHhhc
Q 025225          234 --KDFEELFPE-KHAYDPPEEIFG  254 (256)
Q Consensus       234 --~~~~~~~p~-~~~~~~li~~y~  254 (256)
                        .....+.|+ ...|..+..+|.
T Consensus       572 ~~~~~l~~~p~~~~~~~~l~~~~~  595 (597)
T 2xpi_A          572 HLHESLAISPNEIMASDLLKRALE  595 (597)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHTTC
T ss_pred             HHHHHHhcCCCChHHHHHHHHHHh
Confidence              333455665 445666666554

>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=99.48  E-value=8.9e-13  Score=111.12  Aligned_cols=154  Identities=13%  Similarity=0.078  Sum_probs=113.8

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      +..+-..+...|+.++|+..+.+......-.+... .+...+.+.|++++|.+.|+++.+..  +.+..+|..+...|.+
T Consensus       206 ~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~  283 (388)
T 1w3b_A          206 YINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANALKE  283 (388)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHH
Confidence            33444556667777777644432222211111111 47778888899999999999888775  4567788899999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .|++++|.+.|+++.+.. +.+..+|+.+...|.+.|++++|.+.|+++.+.. +.+..++..+...|.+.|++++|.+
T Consensus       284 ~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~  360 (388)
T 1w3b_A          284 KGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALM  360 (388)
T ss_dssp             HSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHH
T ss_pred             cCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            999999999999888742 3467888899999999999999999999887652 3356788889999999999999888

>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=99.43  E-value=3.1e-12  Score=107.74  Aligned_cols=238  Identities=12%  Similarity=0.027  Sum_probs=153.7

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccc-----------
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRG-----------   68 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~-----------   68 (256)
                      +|.+.|+.+.|.+.|+.+.+...     |..+...+...++...+     +..|+++....+.......           
T Consensus        76 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~p~~~~~~~~l~~~~~~~g~  150 (388)
T 1w3b_A           76 VYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGA-----VQAYVSALQYNPDLYCVRSDLGNLLKALGR  150 (388)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHH-----HHHHHHHHHHCTTCTHHHHHHHHHHHTTSC
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHhCCCcHHHHHHHHHHHHHccC
Confidence            35566677777777776543211     44455555555555555     5555555433221100000           


Q ss_pred             --------------ccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHH
Q 025225           69 --------------KKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFD  130 (256)
Q Consensus        69 --------------~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~  130 (256)
                                    ..-....+..+...+.+.|+.++|+..+ +...+.  .|+..    .+-..+...|++++|...|+
T Consensus       151 ~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~-~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~  227 (388)
T 1w3b_A          151 LEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHF-EKAVTL--DPNFLDAYINLGNVLKEARIFDRAVAAYL  227 (388)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHH-HHHHHH--CTTCHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHH-HHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                          0000123334445566666676666433 333332  23221    35556666777777777777


Q ss_pred             HHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC
Q 025225          131 IIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP  209 (256)
Q Consensus       131 ~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  209 (256)
                      +..+..  +-+..+|..+...|.+.|++++|.+.|+++.+.  .| +..+|+.+...|.+.|++++|.+.|+++.+. .+
T Consensus       228 ~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p  302 (388)
T 1w3b_A          228 RALSLS--PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CP  302 (388)
T ss_dssp             HHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CT
T ss_pred             HHHhhC--cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-Cc
Confidence            776664  446889999999999999999999999999885  34 4678999999999999999999999999876 24


Q ss_pred             CChhHHHHHHHHhcCCCChHHHHHhhh--hhcCCC-cccccchhHhhcc
Q 025225          210 PEELPFRILLKGLLPHPLLRSKVKKDF--EELFPE-KHAYDPPEEIFGK  255 (256)
Q Consensus       210 p~~~t~~~li~~~~~~g~~~~a~~~~~--~~~~p~-~~~~~~li~~y~~  255 (256)
                      ++..+|+.+...+.+.|++++|.+...  ....|+ ..++..+..+|.+
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  351 (388)
T 1w3b_A          303 THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ  351 (388)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHH
Confidence            577899999999999999999988333  233454 4466666666543

>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=99.35  E-value=4.4e-12  Score=108.62  Aligned_cols=180  Identities=9%  Similarity=-0.035  Sum_probs=87.8

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .+.+.|+.+.|.++|+.+.+...     |..+...+...++...+     +..|+++....+..         ...+..+
T Consensus        35 ~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~p~~---------~~~~~~l  100 (450)
T 2y4t_A           35 KLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAA-----LPDLTKVIQLKMDF---------TAARLQR  100 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHhcCCCc---------HHHHHHH
Confidence            34566777777777776643221     44455555556666666     66666655433221         2233344


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-------HH------------HHHHHHcCCHHHHHHHHHHHHhcCCCCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-------AV------------LIELERQEETILAVKIFDIIRKQDWYQP  140 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~l------------i~~~~~~~~~~~a~~~~~~m~~~~~~~p  140 (256)
                      ...|.+.|+.++|...+ +.+....  |+..       .+            -..+.+.|++++|...|+++.+..  ..
T Consensus       101 ~~~~~~~g~~~~A~~~~-~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~  175 (450)
T 2y4t_A          101 GHLLLKQGKLDEAEDDF-KKVLKSN--PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC--VW  175 (450)
T ss_dssp             HHHHHHTTCHHHHHHHH-HHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TT
T ss_pred             HHHHHHcCCHHHHHHHH-HHHHhcC--CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC
Confidence            45556666666665332 3333221  2110       11            122444555555555555555443  33


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +..++..+...|.+.|++++|.+.|+++.+.. +.+..+|..+...|.+.|++++|.+.|+++.
T Consensus       176 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  238 (450)
T 2y4t_A          176 DAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECL  238 (450)
T ss_dssp             CHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44555555555555555555555555544321 1234445555555555555555555555444

>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=99.34  E-value=8.6e-12  Score=106.77  Aligned_cols=237  Identities=11%  Similarity=0.042  Sum_probs=145.3

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCc--cccccccc----
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSL--WRGKKLIG----   73 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~--~~~~~~~~----   73 (256)
                      .+.+.|+.+.|.+.|+.+.+.+.     |..+...+...++...+     +..|+++....+....  ..+..+..    
T Consensus        69 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  143 (450)
T 2y4t_A           69 VFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEA-----EDDFKKVLKSNPSENEEKEAQSQLIKSDEM  143 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHTSCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHhcCCCChhhHHHHHHHHHHHHH
Confidence            46678999999999998765432     66666777778888888     9999888765432210  01110000    


Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      .........+.+.|+.++|+..+ +.+.... -.+... .+..++.+.|++++|.+.|+++.+..  ..+..+|..+...
T Consensus       144 ~~~~~~a~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~  220 (450)
T 2y4t_A          144 QRLRSQALNAFGSGDYTAAIAFL-DKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK--NDNTEAFYKISTL  220 (450)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH--CSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHH-HHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH
Confidence            01112233467777888877444 4443322 111111 46677777788888888888777664  5567777777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCH-hhHHHH------------HHHHHHcCChhHHHHHHHHHHhCCCCCC-----hh
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDS-QTYTEV------------IRGFLKDGSPADAMNIYEDMIKSPDPPE-----EL  213 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~l------------i~~~~~~g~~~~a~~~~~~M~~~g~~p~-----~~  213 (256)
                      |...|++++|.+.|+++.+.  .|+. ..+..+            ...|.+.|++++|.++|+++.+.  .|+     ..
T Consensus       221 ~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~  296 (450)
T 2y4t_A          221 YYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVR  296 (450)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh--CCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHH
Confidence            88888888888887777653  3433 333333            66777777777777777777663  333     34


Q ss_pred             HHHHHHHHhcCCCChHHHHHhhh--hhcCCC-cccccchhHhh
Q 025225          214 PFRILLKGLLPHPLLRSKVKKDF--EELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       214 t~~~li~~~~~~g~~~~a~~~~~--~~~~p~-~~~~~~li~~y  253 (256)
                      .|..+...+.+.|++++|++...  -.+.|+ ...|..+..+|
T Consensus       297 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~  339 (450)
T 2y4t_A          297 SKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAEAY  339 (450)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            66677777777777777777222  223443 34454444443

>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=99.31  E-value=1.1e-12  Score=111.34  Aligned_cols=185  Identities=7%  Similarity=-0.013  Sum_probs=60.9

Q ss_pred             ccccCCchHHHHHHHHHhcCCCccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhc
Q 025225            6 FSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKR   85 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~   85 (256)
                      ..+.|..+.|.++++.+....+|..+..++.+.+++..+     ++.|...      ++        ...+..++..+..
T Consensus        13 l~~~~~ld~A~~fae~~~~~~vWs~La~A~l~~g~~~eA-----Idsfika------~D--------~~~y~~V~~~ae~   73 (449)
T 1b89_A           13 IEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEA-----IDSYIKA------DD--------PSSYMEVVQAANT   73 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHccCHHHHHHHHHhCCChHHHHHHHHHHHHcCCHHHH-----HHHHHcC------CC--------HHHHHHHHHHHHh
Confidence            456788999999999998877899999999999999999     9999532      11        1234445677888


Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQV  164 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~  164 (256)
                      .|+.++|+. ++++..+..-.|.+. .++.+|.+.|+++++.++++        .|+..+|+.+...|...|.+++|...
T Consensus        74 ~g~~EeAi~-yl~~ark~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~--------~pn~~a~~~IGd~~~~~g~yeeA~~~  144 (449)
T 1b89_A           74 SGNWEELVK-YLQMARKKARESYVETELIFALAKTNRLAELEEFIN--------GPNNAHIQQVGDRCYDEKMYDAAKLL  144 (449)
T ss_dssp             ------------------------------------CHHHHTTTTT--------CC----------------CTTTHHHH
T ss_pred             CCCHHHHHH-HHHHHHHhCccchhHHHHHHHHHHhCCHHHHHHHHc--------CCcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999984 665555432222223 48999999999999887774        36777999999999999999999999


Q ss_pred             HHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          165 WESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       165 ~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |..+         ..|..+..++.+.|++++|.+.+.++      .+..||..++.+|...|+++.|..
T Consensus       145 Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~  198 (449)
T 1b89_A          145 YNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQM  198 (449)
T ss_dssp             HHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHH
Confidence            9876         47888888888888888888888887      267888888888888888887755

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.25  E-value=2.2e-11  Score=101.39  Aligned_cols=212  Identities=10%  Similarity=0.029  Sum_probs=159.5

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .+.+.|+.+.|.+.++.+.+...     |..+-..+...++...+     +..|++.....+..         ...+..+
T Consensus        73 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~~~~---------~~~~~~l  138 (368)
T 1fch_A           73 RRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLA-----ISALRRCLELKPDN---------QTALMAL  138 (368)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHH-----HHHHHHHHhcCCCC---------HHHHHHH
Confidence            34567889999999998765432     55555566677777777     88887776543221         2345556


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccC-CCcHHH----------------HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLL-KMDIVA----------------VLIELERQEETILAVKIFDIIRKQDWYQPDA  142 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~----------------li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  142 (256)
                      ...+...|+.++|+..+ +......- .+....                .+..+...|++++|...|+++.+..+-.++.
T Consensus       139 ~~~~~~~g~~~~A~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~  217 (368)
T 1fch_A          139 AVSFTNESLQRQACEIL-RDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDP  217 (368)
T ss_dssp             HHHHHHTTCHHHHHHHH-HHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCH
T ss_pred             HHHHHHcCCHHHHHHHH-HHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccH
Confidence            77888999999998555 44443221 111111                2555558899999999999998886222268


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      .+|..+...|.+.|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+.|++..+.. +.+...+..+...|
T Consensus       218 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~  295 (368)
T 1fch_A          218 DVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISC  295 (368)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            999999999999999999999999988742 2357899999999999999999999999988752 24577899999999


Q ss_pred             cCCCChHHHHH
Q 025225          223 LPHPLLRSKVK  233 (256)
Q Consensus       223 ~~~g~~~~a~~  233 (256)
                      .+.|++++|.+
T Consensus       296 ~~~g~~~~A~~  306 (368)
T 1fch_A          296 INLGAHREAVE  306 (368)
T ss_dssp             HHHTCHHHHHH
T ss_pred             HHCCCHHHHHH
Confidence            99999999988

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.25  E-value=9.6e-12  Score=103.79  Aligned_cols=210  Identities=9%  Similarity=0.030  Sum_probs=159.9

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      .+.+.|+.+.|.+.|+.+.+...     |..+-..+...++...+     +..|++.....+..         ...+..+
T Consensus        74 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A-----~~~~~~al~~~p~~---------~~~~~~l  139 (365)
T 4eqf_A           74 KRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAA-----IVALQRCLELQPNN---------LKALMAL  139 (365)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHhcCCCC---------HHHHHHH
Confidence            35567899999999998754322     66666677778888887     88888776543322         3455666


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH--------------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV--------------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIY  145 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--------------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y  145 (256)
                      ...|.+.|+.++|+..+ +...+.  .|+..              .+...+.+.|++++|.+.|+++.+..+-.++..+|
T Consensus       140 ~~~~~~~g~~~~A~~~~-~~al~~--~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~  216 (365)
T 4eqf_A          140 AVSYTNTSHQQDACEAL-KNWIKQ--NPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQ  216 (365)
T ss_dssp             HHHHHHTTCHHHHHHHH-HHHHHH--CHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHH
T ss_pred             HHHHHccccHHHHHHHH-HHHHHh--CccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHH
Confidence            78889999999998554 444332  12221              24677888999999999999999886222379999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          146 KDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       146 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                      ..+...|...|++++|.+.|++..+.. +.+..+|+.+...|.+.|++++|.+.|++..+.. +.+..+|..+...|.+.
T Consensus       217 ~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~  294 (365)
T 4eqf_A          217 TGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINL  294 (365)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHC
Confidence            999999999999999999999988742 2357899999999999999999999999988762 22478899999999999


Q ss_pred             CChHHHHH
Q 025225          226 PLLRSKVK  233 (256)
Q Consensus       226 g~~~~a~~  233 (256)
                      |++++|.+
T Consensus       295 g~~~~A~~  302 (365)
T 4eqf_A          295 GAYREAVS  302 (365)
T ss_dssp             TCCHHHHH
T ss_pred             CCHHHHHH
Confidence            99999988

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.23  E-value=4.5e-11  Score=97.55  Aligned_cols=209  Identities=10%  Similarity=0.028  Sum_probs=157.2

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +.+.|+.+.|.++++.+.+...     |..+-..+...++...+     +..|++.....+..         ...+..+.
T Consensus        31 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~a~~~~~~~---------~~~~~~la   96 (327)
T 3cv0_A           31 MLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLA-----IIALNHARMLDPKD---------IAVHAALA   96 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHhcCcCC---------HHHHHHHH
Confidence            4567889999999998754332     55555566667777777     88887776543221         23445566


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhcc-CCCcHHHHH--------------HH--HHHcCCHHHHHHHHHHHHhcCCCCCCHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRL-LKMDIVAVL--------------IE--LERQEETILAVKIFDIIRKQDWYQPDAY  143 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~li--------------~~--~~~~~~~~~a~~~~~~m~~~~~~~p~~~  143 (256)
                      ..+...|+.++|...+ +...... -.+.....+              ..  +...|++++|.+.+++..+..  ..+..
T Consensus        97 ~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~  173 (327)
T 3cv0_A           97 VSHTNEHNANAALASL-RAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN--PNDAQ  173 (327)
T ss_dssp             HHHHHTTCHHHHHHHH-HHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS--TTCHH
T ss_pred             HHHHHcCCHHHHHHHH-HHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC--CCCHH
Confidence            7788999999998555 4444322 111211222              33  677899999999999999886  56889


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhc
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLL  223 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~  223 (256)
                      ++..+...|...|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+.|++..+.. +.+...|..+...|.
T Consensus       174 ~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~  251 (327)
T 3cv0_A          174 LHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYS  251 (327)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHH
Confidence            99999999999999999999999988742 2357889999999999999999999999988753 235778999999999


Q ss_pred             CCCChHHHHH
Q 025225          224 PHPLLRSKVK  233 (256)
Q Consensus       224 ~~g~~~~a~~  233 (256)
                      +.|++++|.+
T Consensus       252 ~~g~~~~A~~  261 (327)
T 3cv0_A          252 NMSQYDLAAK  261 (327)
T ss_dssp             HTTCHHHHHH
T ss_pred             HhccHHHHHH
Confidence            9999999988

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.20  E-value=3.1e-10  Score=92.62  Aligned_cols=154  Identities=8%  Similarity=-0.011  Sum_probs=86.3

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      +..+...+...|+.++|+..+ +...... -.+... .+-..+...|++++|.+.|++..+..  +.+..++..+...|.
T Consensus       128 ~~~l~~~~~~~~~~~~A~~~~-~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~  204 (330)
T 3hym_B          128 WIAYGHSFAVESEHDQAMAAY-FTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA--PEDPFVMHEVGVVAF  204 (330)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHH-HHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHH-HHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC--CCChHHHHHHHHHHH
Confidence            334445555666666665433 2322211 111111 34555566666666666666666554  445666666666666


Q ss_pred             hcCCHHHHHHHHHHHHhCC--------CCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          154 RTGKMNEAMQVWESMRKED--------LFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g--------~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                      ..|++++|.+.|++..+..        ...+..+|..+...|.+.|++++|.+.|++..+.. ..+...|..+...|.+.
T Consensus       205 ~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~  283 (330)
T 3hym_B          205 QNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLM  283 (330)
T ss_dssp             HTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHH
T ss_pred             HcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHh
Confidence            6666666666666655421        12234566666666666666666666666665442 12445566666666666


Q ss_pred             CChHHHHH
Q 025225          226 PLLRSKVK  233 (256)
Q Consensus       226 g~~~~a~~  233 (256)
                      |++++|.+
T Consensus       284 g~~~~A~~  291 (330)
T 3hym_B          284 GNFENAVD  291 (330)
T ss_dssp             TCHHHHHH
T ss_pred             ccHHHHHH
Confidence            66666666

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.19  E-value=3.6e-10  Score=92.24  Aligned_cols=230  Identities=9%  Similarity=-0.102  Sum_probs=165.3

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +-..|+.+.|.++++.+.+...     +..+...+...++...+     +..++++....+..         ...+..+.
T Consensus        32 ~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l~   97 (330)
T 3hym_B           32 HYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANEL-----FYLSHKLVDLYPSN---------PVSWFAVG   97 (330)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHH-----HHHHHHHHHHCTTS---------THHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHH-----HHHHHHHHHhCcCC---------HHHHHHHH
Confidence            3456899999999998754332     33344445555666666     88887776543322         23445556


Q ss_pred             HHhhcCC-CcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           81 LGLKRFK-DDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        81 ~~~~~~~-~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      ..+...| +.++|...+ +...... -.+... .+-..+...|++++|.+.|++..+..  ..+...+..+...|...|+
T Consensus        98 ~~~~~~~~~~~~A~~~~-~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~  174 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYL-SKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM--KGCHLPMLYIGLEYGLTNN  174 (330)
T ss_dssp             HHHHHSCSCHHHHHHHH-HHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCSHHHHHHHHHHHHTTC
T ss_pred             HHHHHhhhhHHHHHHHH-HHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc--cccHHHHHHHHHHHHHHhh
Confidence            7778888 899998544 4444332 222222 57888899999999999999999886  4566778889999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC--------CCCChhHHHHHHHHhcCCCChH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP--------DPPEELPFRILLKGLLPHPLLR  229 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g--------~~p~~~t~~~li~~~~~~g~~~  229 (256)
                      +++|.+.|++..+.. +.+...|..+...|.+.|++++|...|++..+..        ...+...|..+...|.+.|+++
T Consensus       175 ~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  253 (330)
T 3hym_B          175 SKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYA  253 (330)
T ss_dssp             HHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHH
Confidence            999999999988753 2357889999999999999999999999887531        1344678999999999999999


Q ss_pred             HHHHhhh--hhcCCC-cccccchhHhh
Q 025225          230 SKVKKDF--EELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       230 ~a~~~~~--~~~~p~-~~~~~~li~~y  253 (256)
                      +|.+...  ..+.|+ ...|..+..+|
T Consensus       254 ~A~~~~~~a~~~~~~~~~~~~~la~~~  280 (330)
T 3hym_B          254 EALDYHRQALVLIPQNASTYSAIGYIH  280 (330)
T ss_dssp             HHHHHHHHHHHHSTTCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCccchHHHHHHHHHH
Confidence            9998322  233443 34455554444

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.14  E-value=8.2e-09  Score=80.48  Aligned_cols=196  Identities=8%  Similarity=-0.035  Sum_probs=139.1

Q ss_pred             ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CC
Q 025225           28 KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LK  106 (256)
Q Consensus        28 ~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~  106 (256)
                      |..+-..+...++...+     +..|++.....+..         ...+..+...+.+.|+.++|+..+ +...... -.
T Consensus        26 ~~~~a~~~~~~~~~~~A-----~~~~~~~l~~~~~~---------~~~~~~la~~~~~~~~~~~A~~~~-~~~~~~~~~~   90 (243)
T 2q7f_A           26 GGQQMGRGSEFGDYEKA-----AEAFTKAIEENKED---------AIPYINFANLLSSVNELERALAFY-DKALELDSSA   90 (243)
T ss_dssp             ----------------C-----CTTHHHHHTTCTTC---------HHHHHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTC
T ss_pred             HHHHHHHHHHhhCHHHH-----HHHHHHHHHhCccc---------HHHHHHHHHHHHHcCCHHHHHHHH-HHHHHcCCcc
Confidence            44444455566777777     88888776643322         234445567788999999998655 4443332 11


Q ss_pred             CcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 025225          107 MDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIR  185 (256)
Q Consensus       107 ~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  185 (256)
                      +... .+...+...|++++|.+.|++..+..  ..+...|..+...|.+.|++++|.+.+++..+.. ..+...+..+..
T Consensus        91 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  167 (243)
T 2q7f_A           91 ATAYYGAGNVYVVKEMYKEAKDMFEKALRAG--MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGM  167 (243)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHH
Confidence            2222 47778889999999999999999886  6688899999999999999999999999988742 236788999999


Q ss_pred             HHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCC
Q 025225          186 GFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPE  242 (256)
Q Consensus       186 ~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~  242 (256)
                      .|.+.|++++|.+.|++..+.. ..+..++..+...|.+.|++++|.+  .......|+
T Consensus       168 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~  225 (243)
T 2q7f_A          168 CLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPD  225 (243)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTT
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcc
Confidence            9999999999999999988653 2357789999999999999999988  233344554

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.11  E-value=4e-10  Score=91.86  Aligned_cols=221  Identities=10%  Similarity=-0.046  Sum_probs=156.2

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccc---cchhH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKL---IGKEA   76 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~---~~~~~   76 (256)
                      .+.+.|+.+.|.+.++...+...     +..+-..+...++...+     +..++......+..........   .....
T Consensus        64 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (327)
T 3cv0_A           64 TQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAA-----LASLRAWLLSQPQYEQLGSVNLQADVDIDD  138 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHTSTTTTTC-------------
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHhCCccHHHHHHHhHHHHHHHH
Confidence            45678899999999998754322     44555556667777777     8888777654332211110000   00000


Q ss_pred             HHHH-H--HhhcCCCcHHHHHHHHHHHhhccC-CCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           77 LFVI-L--GLKRFKDDEEKLQKFIKTHVLRLL-KMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        77 ~~~i-~--~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      ...+ .  .+...|+.++|...+ +......- .+... .+...+.+.|++++|.+.+++..+..  ..+..+|..+...
T Consensus       139 ~~~~~~~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~  215 (327)
T 3cv0_A          139 LNVQSEDFFFAAPNEYRECRTLL-HAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR--PDDAQLWNKLGAT  215 (327)
T ss_dssp             -------CCTTSHHHHHHHHHHH-HHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHcccHHHHHHHH-HHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCcHHHHHHHHHH
Confidence            0001 2  266778888988544 44443321 12222 47788899999999999999999886  5678999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-----------ChhHHHHHHH
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-----------EELPFRILLK  220 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-----------~~~t~~~li~  220 (256)
                      |...|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+.|++..+....+           +...|..+..
T Consensus       216 ~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~  294 (327)
T 3cv0_A          216 LANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRM  294 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHH
Confidence            999999999999999988742 2357889999999999999999999999987653221           5788999999


Q ss_pred             HhcCCCChHHHHHh
Q 025225          221 GLLPHPLLRSKVKK  234 (256)
Q Consensus       221 ~~~~~g~~~~a~~~  234 (256)
                      .|.+.|+.++|...
T Consensus       295 ~~~~~g~~~~A~~~  308 (327)
T 3cv0_A          295 LLNVMNRPDLVELT  308 (327)
T ss_dssp             HHHHTTCHHHHHHH
T ss_pred             HHHhcCCHHHHHHH
Confidence            99999999999883

>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=99.11  E-value=6.6e-09  Score=81.72  Aligned_cols=154  Identities=15%  Similarity=0.100  Sum_probs=103.3

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      +..+...+...|+.++|+..+ +...... -.+... .+-..+...|++++|.+.|++..+..  ..+...|..+...|.
T Consensus        40 ~~~~a~~~~~~~~~~~A~~~~-~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~  116 (252)
T 2ho1_A           40 YIQLGLGYLQRGNTEQAKVPL-RKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD--SRNARVLNNYGGFLY  116 (252)
T ss_dssp             HHHHHHHHHHTTCTGGGHHHH-HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHH-HHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHH
Confidence            344455667778888877444 3433322 111111 35666777788888888888777765  456777777778888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ..|++++|.+.|++..+.+..| +...|..+...|.+.|++++|.+.|++..+.. ..+...+..+...|...|++++|.
T Consensus       117 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~  195 (252)
T 2ho1_A          117 EQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPAR  195 (252)
T ss_dssp             HTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHH
Confidence            8888888888888777643344 34667777777778888888888887776542 224566777777777788877777


Q ss_pred             H
Q 025225          233 K  233 (256)
Q Consensus       233 ~  233 (256)
                      +
T Consensus       196 ~  196 (252)
T 2ho1_A          196 Q  196 (252)
T ss_dssp             H
T ss_pred             H
Confidence            7

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.10  E-value=1.4e-10  Score=96.73  Aligned_cols=221  Identities=11%  Similarity=-0.018  Sum_probs=156.7

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccccc-ccchhHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKK-LIGKEALF   78 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~-~~~~~~~~   78 (256)
                      .|.+.|+.+.|.+.|+...+...     |..+-..+...++...+     +..|++.....+......... ........
T Consensus       108 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~p~~~~~~~~~~~~~~~~~~  182 (365)
T 4eqf_A          108 TQAENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDA-----CEALKNWIKQNPKYKYLVKNKKGSPGLTRR  182 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCHHHHCC-------------
T ss_pred             HHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHH-----HHHHHHHHHhCccchHHHhhhccchHHHHH
Confidence            46678999999999998754322     66666677778888877     888877765432211111000 00112223


Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhcc-C--CCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRL-L--KMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~-~--~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      +...+.+.|+.++|+..+ +...... -  .+... .+-..+...|++++|.+.|++..+..  +.+..+|+.+...|..
T Consensus       183 l~~~~~~~g~~~~A~~~~-~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~  259 (365)
T 4eqf_A          183 MSKSPVDSSVLEGVKELY-LEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR--PEDYSLWNRLGATLAN  259 (365)
T ss_dssp             ------CCHHHHHHHHHH-HHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhhhHHHHHHHH-HHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHH
Confidence            356778899999998555 4544432 2  12222 57888899999999999999999886  6689999999999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC---C--------CCChhHHHHHHHHh
Q 025225          155 TGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP---D--------PPEELPFRILLKGL  222 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g---~--------~p~~~t~~~li~~~  222 (256)
                      .|++++|.+.|++..+.  .| +..+|..+...|.+.|++++|.+.|++..+..   .        ..+...|..+-.++
T Consensus       260 ~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  337 (365)
T 4eqf_A          260 GDRSEEAVEAYTRALEI--QPGFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIAL  337 (365)
T ss_dssp             TTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHH
Confidence            99999999999998874  35 47889999999999999999999999987541   1        11478899999999


Q ss_pred             cCCCChHHHHHhh
Q 025225          223 LPHPLLRSKVKKD  235 (256)
Q Consensus       223 ~~~g~~~~a~~~~  235 (256)
                      ...|+.+.+.+..
T Consensus       338 ~~~g~~~~a~~~~  350 (365)
T 4eqf_A          338 SLMDQPELFQAAN  350 (365)
T ss_dssp             HHHTCHHHHHHHH
T ss_pred             HHcCcHHHHHHHH
Confidence            9999988777643

>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=99.09  E-value=4e-09  Score=83.01  Aligned_cols=195  Identities=9%  Similarity=0.058  Sum_probs=143.4

Q ss_pred             ccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-H
Q 025225           34 AFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-A  111 (256)
Q Consensus        34 a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~  111 (256)
                      .+...++...+     +..|++.....+..         ...+..+...+.+.|+.++|...+ +...... -.+... .
T Consensus        46 ~~~~~~~~~~A-----~~~~~~al~~~~~~---------~~~~~~la~~~~~~~~~~~A~~~~-~~a~~~~~~~~~~~~~  110 (252)
T 2ho1_A           46 GYLQRGNTEQA-----KVPLRKALEIDPSS---------ADAHAALAVVFQTEMEPKLADEEY-RKALASDSRNARVLNN  110 (252)
T ss_dssp             HHHHTTCTGGG-----HHHHHHHHHHCTTC---------HHHHHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCHHHHHH
T ss_pred             HHHHcCChHHH-----HHHHHHHHhcCCCh---------HHHHHHHHHHHHHcCCHHHHHHHH-HHHHHHCcCcHHHHHH
Confidence            33445566666     77777665443221         234455567788999999998555 4443332 122222 4


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQP-DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      +...+...|++++|.+.|++..+.+ ..| +...|..+...|...|++++|.+.|++..+.. ..+...|..+...|.+.
T Consensus       111 la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~  188 (252)
T 2ho1_A          111 YGGFLYEQKRYEEAYQRLLEASQDT-LYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKE  188 (252)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHTTCT-TCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHhCc-cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHc
Confidence            7788889999999999999998833 334 67788999999999999999999999988743 23578899999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCcccc
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAY  246 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~  246 (256)
                      |++++|.++|++..+.. ..+...+..+...|...|+.++|.+  .......|+...+
T Consensus       189 g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~  245 (252)
T 2ho1_A          189 REYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYPGSLEY  245 (252)
T ss_dssp             TCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSHHH
T ss_pred             CCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCHHH
Confidence            99999999999988753 3566778889999999999999988  3334455654433

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.08  E-value=4.2e-10  Score=91.61  Aligned_cols=205  Identities=10%  Similarity=0.005  Sum_probs=115.8

Q ss_pred             cccccCCchHHHHHHHHHhcCCC---ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS---KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVIL   81 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~---~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~   81 (256)
                      +|-..|+++.|+.-++.. ..+.   +..+...+...++.+.+     +..++++......|+.       ...+..+-.
T Consensus        43 ~yi~~g~~~~al~~~~~~-~~~~~~a~~~la~~~~~~~~~~~A-----~~~l~~ll~~~~~P~~-------~~~~~~la~  109 (291)
T 3mkr_A           43 AYLAQRKYGVVLDEIKPS-SAPELQAVRMFAEYLASHSRRDAI-----VAELDREMSRSVDVTN-------TTFLLMAAS  109 (291)
T ss_dssp             HHHHTTCHHHHHHHSCTT-SCHHHHHHHHHHHHHHCSTTHHHH-----HHHHHHHHHSCCCCSC-------HHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHhccc-CChhHHHHHHHHHHHcCCCcHHHH-----HHHHHHHHhcccCCCC-------HHHHHHHHH
Confidence            344455565555544332 1111   34444444555555555     6666665543322210       112223345


Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHH---HHHHHHHHhcCC
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIY---KDLIIALARTGK  157 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y---~~li~~~~~~g~  157 (256)
                      .+.+.|+.++|+..+ +.    +-.++.. .+...+.+.|++++|.+.|+++.+..   |+...+   ...+..+...|+
T Consensus       110 ~~~~~g~~~~Al~~l-~~----~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~---p~~~~~~l~~a~~~l~~~~~~  181 (291)
T 3mkr_A          110 IYFYDQNPDAALRTL-HQ----GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD---EDATLTQLATAWVSLAAGGEK  181 (291)
T ss_dssp             HHHHTTCHHHHHHHH-TT----CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---TTCHHHHHHHHHHHHHHCTTH
T ss_pred             HHHHCCCHHHHHHHH-hC----CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC---cCcHHHHHHHHHHHHHhCchH
Confidence            667777777776433 22    1112222 36667777777888888777777664   332211   223333344577


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      +++|..+|+++.+. .+.+...|+.+-..|.+.|++++|.+.|++..+.. +-+..++..++..+...|+.+++.
T Consensus       182 ~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~~~l~~l~~~~~~~g~~~eaa  254 (291)
T 3mkr_A          182 LQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHPETLINLVVLSQHLGKPPEVT  254 (291)
T ss_dssp             HHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCCHHHH
Confidence            77888888777765 33466777777777777788888888777766542 225556777777777777766543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.07  E-value=2.3e-08  Score=76.78  Aligned_cols=154  Identities=11%  Similarity=-0.027  Sum_probs=102.3

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      +..+...+...|+.++|+..+ +...+.. -.+... .+...+...|++++|.+.|++..+..  ..+..+|..+...|.
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~   87 (225)
T 2vq2_A           11 KTQLAMEYMRGQDYRQATASI-EDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK--PDSAEINNNYGWFLC   87 (225)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHH-HHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC--CCChHHHHHHHHHHH
Confidence            344456667778888877444 3333322 111222 35666777788888888888777664  456777777777788


Q ss_pred             hc-CCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHH
Q 025225          154 RT-GKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSK  231 (256)
Q Consensus       154 ~~-g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a  231 (256)
                      .. |++++|.+.|+++.+.+..|+ ...|..+...|.+.|++++|.+.|++..+.. ..+...+..+...|.+.|++++|
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  166 (225)
T 2vq2_A           88 GRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDA  166 (225)
T ss_dssp             TTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHH
Confidence            88 888888888887776323333 4667777777777888888888887776542 12356677777777777877777


Q ss_pred             HH
Q 025225          232 VK  233 (256)
Q Consensus       232 ~~  233 (256)
                      .+
T Consensus       167 ~~  168 (225)
T 2vq2_A          167 DY  168 (225)
T ss_dssp             HH
T ss_pred             HH
Confidence            77

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.07  E-value=5.9e-10  Score=92.65  Aligned_cols=220  Identities=13%  Similarity=-0.019  Sum_probs=156.5

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCcccccc------ccc
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKK------LIG   73 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~------~~~   73 (256)
                      .+.+.|+.+.|.+.++...+...     +..+...+...++...+     +..|++.....+.........      ...
T Consensus       107 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (368)
T 1fch_A          107 TQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQA-----CEILRDWLRYTPAYAHLVTPAEEGAGGAGL  181 (368)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHTSTTTGGGCC-----------
T ss_pred             HHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHhCcCcHHHHHHHHHHhhhhcc
Confidence            45678899999999998654322     55555666677777777     888877765543321111100      000


Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCC-CcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLK-MDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      ......+..+...|+.++|+..+ +......-. ++..   .+-..+.+.|++++|...|++..+..  +.+..+|..+.
T Consensus       182 ~~~~~~~~~~~~~~~~~~A~~~~-~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~l~  258 (368)
T 1fch_A          182 GPSKRILGSLLSDSLFLEVKELF-LAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR--PNDYLLWNKLG  258 (368)
T ss_dssp             ----CTTHHHHHHHHHHHHHHHH-HHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             cHHHHHHHHHhhcccHHHHHHHH-HHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cCCHHHHHHHH
Confidence            00000122233778899998554 444443221 1222   47888899999999999999999885  56789999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC---CC-------ChhHHHHHH
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD---PP-------EELPFRILL  219 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~---~p-------~~~t~~~li  219 (256)
                      ..|...|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+.|++..+...   .|       ...+|..+.
T Consensus       259 ~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~  337 (368)
T 1fch_A          259 ATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLR  337 (368)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHH
Confidence            99999999999999999988742 23578899999999999999999999999875421   11       268899999


Q ss_pred             HHhcCCCChHHHHH
Q 025225          220 KGLLPHPLLRSKVK  233 (256)
Q Consensus       220 ~~~~~~g~~~~a~~  233 (256)
                      .+|...|+.++|..
T Consensus       338 ~~~~~~g~~~~A~~  351 (368)
T 1fch_A          338 LALSMLGQSDAYGA  351 (368)
T ss_dssp             HHHHHHTCGGGHHH
T ss_pred             HHHHHhCChHhHHH
Confidence            99999999999877

>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=99.06  E-value=2.5e-10  Score=97.00  Aligned_cols=196  Identities=12%  Similarity=-0.006  Sum_probs=89.9

Q ss_pred             cccccccCCchHHHHHHHHHhcCCCccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHH
Q 025225            3 TRLFSRSKIPILASIVLQNLTKNPSKNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILG   82 (256)
Q Consensus         3 i~~~~~~~~~~~A~~l~~~m~~~~~~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~   82 (256)
                      ..++.+.|+.++|++.|.+......|..+..++...+..+++     +..++..++..  ++        ......++.+
T Consensus        39 a~A~l~~g~~~eAIdsfika~D~~~y~~V~~~ae~~g~~EeA-----i~yl~~ark~~--~~--------~~i~~~Li~~  103 (449)
T 1b89_A           39 AKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEEL-----VKYLQMARKKA--RE--------SYVETELIFA  103 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHcCCHHHHHHHHHcCCCHHHHHHHHHHHHhCCCHHHH-----HHHHHHHHHhC--cc--------chhHHHHHHH
Confidence            346778899999999998876655699999999998888888     88665554431  11        1223345788


Q ss_pred             hhcCCCcHHHHHHHHHHHhhccCCCc---HHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRLLKMD---IVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN  159 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~  159 (256)
                      |.+.|++.++. .+++       .|+   ...+-..|...|.+++|...|+.+          ..|..+..++++.|+++
T Consensus       104 Y~Klg~l~e~e-~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a----------~n~~~LA~~L~~Lg~yq  165 (449)
T 1b89_A          104 LAKTNRLAELE-EFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV----------SNFGRLASTLVHLGEYQ  165 (449)
T ss_dssp             -----CHHHHT-TTTT-------CC----------------CTTTHHHHHHHT----------TCHHHHHHHHHTTTCHH
T ss_pred             HHHhCCHHHHH-HHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh----------hhHHHHHHHHHHhccHH
Confidence            99999998875 4543       243   336899999999999999999976          26999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhhhhhc
Q 025225          160 EAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKDFEEL  239 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~  239 (256)
                      +|.+.+.++      .++.+|..++.+|+..|+++.|......+.   +.|+.  ...++..|.+.|.+++++.....++
T Consensus       166 ~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~---~~ad~--l~~lv~~Yek~G~~eEai~lLe~aL  234 (449)
T 1b89_A          166 AAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV---VHADE--LEELINYYQDRGYFEELITMLEAAL  234 (449)
T ss_dssp             HHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT---TCHHH--HHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH---hCHhh--HHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            999999988      378999999999999999999966555422   33443  5579999999999999988555555


Q ss_pred             CCC
Q 025225          240 FPE  242 (256)
Q Consensus       240 ~p~  242 (256)
                      .-|
T Consensus       235 ~le  237 (449)
T 1b89_A          235 GLE  237 (449)
T ss_dssp             TST
T ss_pred             CCc
Confidence            443

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.03  E-value=6.7e-09  Score=89.97  Aligned_cols=211  Identities=8%  Similarity=-0.050  Sum_probs=161.7

Q ss_pred             cccccCCchHHHHHHHHHhcCC--C--ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            5 LFSRSKIPILASIVLQNLTKNP--S--KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~--~--~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      .+.+.|+.+.|.+.++...+..  .  |..+...+...++...+     +..++......+..         ...+..+.
T Consensus       246 ~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l~  311 (514)
T 2gw1_A          246 FKFLKNDPLGAHEDIKKAIELFPRVNSYIYMALIMADRNDSTEY-----YNYFDKALKLDSNN---------SSVYYHRG  311 (514)
T ss_dssp             HHHHSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSSCCTTG-----GGHHHHHHTTCTTC---------THHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCccHHHHHHHHHHHHHCCCHHHH-----HHHHHHHhhcCcCC---------HHHHHHHH
Confidence            3567889999999999865322  2  55555667777888887     89998877654322         23455566


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      ..+...|+.++|+..+ +...... -.+... .+...+...|++++|...|++..+..  ..+..+|..+...|.+.|++
T Consensus       312 ~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~  388 (514)
T 2gw1_A          312 QMNFILQNYDQAGKDF-DKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKF--PEAPEVPNFFAEILTDKNDF  388 (514)
T ss_dssp             HHHHHTTCTTHHHHHH-HHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHTTCH
T ss_pred             HHHHHhCCHHHHHHHH-HHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc--ccCHHHHHHHHHHHHHCCCH
Confidence            7888999999998555 4443322 222322 47778889999999999999998875  55778999999999999999


Q ss_pred             HHHHHHHHHHHhCC-CCCC----HhhHHHHHHHHHH---cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          159 NEAMQVWESMRKED-LFPD----SQTYTEVIRGFLK---DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       159 ~~a~~~~~~m~~~g-~~p~----~~t~~~li~~~~~---~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      ++|.+.|+++.+.. -.|+    ...|..+...|.+   .|++++|.+.|++..+.. ..+..++..+...|.+.|++++
T Consensus       389 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~  467 (514)
T 2gw1_A          389 DKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDE  467 (514)
T ss_dssp             HHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHH
Confidence            99999999987631 1122    3489999999999   999999999999988753 2356788899999999999999


Q ss_pred             HHH
Q 025225          231 KVK  233 (256)
Q Consensus       231 a~~  233 (256)
                      |.+
T Consensus       468 A~~  470 (514)
T 2gw1_A          468 AIT  470 (514)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            988

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.03  E-value=3.9e-09  Score=81.14  Aligned_cols=171  Identities=12%  Similarity=0.025  Sum_probs=128.3

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHc-CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQ-EETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~-~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      .+..+...+...|+.++|...+ +...... -.+... .+...+... |++++|...+++..+.+....+...|..+...
T Consensus        44 ~~~~l~~~~~~~~~~~~A~~~~-~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~  122 (225)
T 2vq2_A           44 AWLVRAEIYQYLKVNDKAQESF-RQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGIC  122 (225)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHH-HHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHH
Confidence            3445566778999999998555 4443322 112222 477888899 99999999999999843123347889999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHH
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSK  231 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a  231 (256)
                      |...|++++|.+.|++..+.. +.+...+..+...|.+.|++++|.+++++..+.....+...+..+...+...|+.+++
T Consensus       123 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a  201 (225)
T 2vq2_A          123 SAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAA  201 (225)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHH
Confidence            999999999999999988742 2257889999999999999999999999988763324677788888888999999888


Q ss_pred             HH--hhhhhcCCCccccc
Q 025225          232 VK--KDFEELFPEKHAYD  247 (256)
Q Consensus       232 ~~--~~~~~~~p~~~~~~  247 (256)
                      ..  .......|+...+.
T Consensus       202 ~~~~~~~~~~~p~~~~~~  219 (225)
T 2vq2_A          202 YEYEAQLQANFPYSEELQ  219 (225)
T ss_dssp             HHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHHhCCCCHHHH
Confidence            77  23334567655443

>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=99.03  E-value=1.6e-08  Score=75.14  Aligned_cols=152  Identities=7%  Similarity=-0.046  Sum_probs=123.0

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      +..+...+...|+.++|+..+ +......- .+..   .+...+...|++++|...+++..+..  ..+...|..+...|
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~   86 (186)
T 3as5_A           11 YRDKGISHAKAGRYSQAVMLL-EQVYDADA-FDVDVALHLGIAYVKTGAVDRGTELLERSLADA--PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHH-TTTCCTTS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHH-HHHHHhCc-cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHH
Confidence            344556778899999998544 44433211 1222   47778889999999999999998885  66889999999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ...|++++|.+.|++..+.. +.+...+..+...|.+.|++++|.+.+++..+.. ..+...+..+...|...|++++|.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999988752 2467888999999999999999999999988763 345788899999999999999998


Q ss_pred             H
Q 025225          233 K  233 (256)
Q Consensus       233 ~  233 (256)
                      +
T Consensus       165 ~  165 (186)
T 3as5_A          165 P  165 (186)
T ss_dssp             H
T ss_pred             H
Confidence            8

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.02  E-value=5.5e-09  Score=81.06  Aligned_cols=150  Identities=11%  Similarity=0.035  Sum_probs=91.1

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHc-----------CCHHHHHHHHHHHHhcCCCCC
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQ-----------EETILAVKIFDIIRKQDWYQP  140 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~-----------~~~~~a~~~~~~m~~~~~~~p  140 (256)
                      +..+-..+.+.|+.++|+..+ +...+.  .|+..    .+-..+...           |++++|...|++..+..  +-
T Consensus        42 ~~~lg~~~~~~g~~~~A~~~~-~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--P~  116 (217)
T 2pl2_A           42 LYWLARTQLKLGLVNPALENG-KTLVAR--TPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN--PR  116 (217)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHH-HHHHHH--CTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC--TT
T ss_pred             HHHHHHHHHHcCCHHHHHHHH-HHHHHh--CCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC--cc
Confidence            333445566777777776444 333222  23221    345555566           77777777777777664  44


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      +...|..+-..|...|++++|...|++..+..  .+...+..+-..|...|++++|...|++..+.. +-+...+..+..
T Consensus       117 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~  193 (217)
T 2pl2_A          117 YAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYAS  193 (217)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            56677777777777777777777777777655  566777777777777777777777777776542 124556667777


Q ss_pred             HhcCCCChHHHHH
Q 025225          221 GLLPHPLLRSKVK  233 (256)
Q Consensus       221 ~~~~~g~~~~a~~  233 (256)
                      .+.+.|++++|.+
T Consensus       194 ~~~~~g~~~~A~~  206 (217)
T 2pl2_A          194 ALLLKGKAEEAAR  206 (217)
T ss_dssp             HHTC---------
T ss_pred             HHHHccCHHHHHH
Confidence            7777777777766

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.00  E-value=1.8e-08  Score=81.96  Aligned_cols=217  Identities=8%  Similarity=-0.026  Sum_probs=149.4

Q ss_pred             cCCchHHHHHHHHHhcCCC------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHH
Q 025225            9 SKIPILASIVLQNLTKNPS------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILG   82 (256)
Q Consensus         9 ~~~~~~A~~l~~~m~~~~~------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~   82 (256)
                      .|..+.|++.++.......      .-.+..++...|+.+.+     +..++.   . ..+        .......+...
T Consensus        12 ~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~a-----l~~~~~---~-~~~--------~~~a~~~la~~   74 (291)
T 3mkr_A           12 IGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVV-----LDEIKP---S-SAP--------ELQAVRMFAEY   74 (291)
T ss_dssp             TTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHH-----HHHSCT---T-SCH--------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHH-----HHHhcc---c-CCh--------hHHHHHHHHHH
Confidence            5677778887776544332      22334555566666666     554432   1 111        01233334567


Q ss_pred             hhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      +++.++.++|+..+ +.+...+..|+..    .+-..+...|++++|++.+++       ..+...+..+...|.+.|++
T Consensus        75 ~~~~~~~~~A~~~l-~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~-------~~~~~~~~~l~~~~~~~g~~  146 (291)
T 3mkr_A           75 LASHSRRDAIVAEL-DREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ-------GDSLECMAMTVQILLKLDRL  146 (291)
T ss_dssp             HHCSTTHHHHHHHH-HHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT-------CCSHHHHHHHHHHHHHTTCH
T ss_pred             HcCCCcHHHHHHHH-HHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCH
Confidence            88889999998554 6666665556433    244778899999999999987       35788999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHhhH---HHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhh
Q 025225          159 NEAMQVWESMRKEDLFPDSQTY---TEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKD  235 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~~t~---~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~  235 (256)
                      ++|.+.|+++.+..  |+....   ...+..+...|++++|..+|+++.+. .+.+...|+.+..+|.+.|++++|.+..
T Consensus       147 ~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l  223 (291)
T 3mkr_A          147 DLARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVL  223 (291)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999998853  664322   22333344458999999999999987 4568889999999999999999999833


Q ss_pred             h--hhcCCC-cccccchhHhh
Q 025225          236 F--EELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       236 ~--~~~~p~-~~~~~~li~~y  253 (256)
                      .  -...|+ ..++..++..+
T Consensus       224 ~~al~~~p~~~~~l~~l~~~~  244 (291)
T 3mkr_A          224 QEALDKDSGHPETLINLVVLS  244 (291)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHhCCCCHHHHHHHHHHH
Confidence            2  334454 44555555443

>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=98.97  E-value=5.2e-08  Score=68.18  Aligned_cols=118  Identities=14%  Similarity=0.180  Sum_probs=70.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +...+...|++++|..+|+++.+..  ..+...|..+...+...|++++|.+.|+++.+.+ ..+...|..+...|.+.|
T Consensus         7 l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~   83 (136)
T 2fo7_A            7 LGNAYYKQGDYDEAIEYYQKALELD--PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQG   83 (136)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHcC--CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhc
Confidence            4445556666666666666666554  3455666666666666666666666666665532 123455666666666666


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++++|.++++++.+.. ..+...+..+...|.+.|++++|.+
T Consensus        84 ~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  124 (136)
T 2fo7_A           84 DYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIE  124 (136)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHH
Confidence            6666666666665542 1234555666666666666666665

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.96  E-value=5.1e-08  Score=75.53  Aligned_cols=169  Identities=11%  Similarity=-0.054  Sum_probs=132.7

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      +..+-..+.+.|+.++|+..+ +...+.  .|+..    .+-..+.+.|++++|...|++..+..  +-+...|..+-..
T Consensus         8 ~~~lg~~~~~~g~~~~A~~~~-~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~   82 (217)
T 2pl2_A            8 PLRLGVQLYALGRYDAALTLF-ERALKE--NPQDPEALYWLARTQLKLGLVNPALENGKTLVART--PRYLGGYMVLSEA   82 (217)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHH-HHHHTT--SSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHH-HHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHH
Confidence            334456778999999998555 444332  24322    46677889999999999999999886  5678899999999


Q ss_pred             HHhc-----------CCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHH
Q 025225          152 LART-----------GKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILL  219 (256)
Q Consensus       152 ~~~~-----------g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li  219 (256)
                      |...           |++++|...|++..+.  .| +...|..+-..|...|++++|...|++..+..  .+...+..+-
T Consensus        83 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la  158 (217)
T 2pl2_A           83 YVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALA  158 (217)
T ss_dssp             HHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_pred             HHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHH
Confidence            9999           9999999999998874  35 46788888899999999999999999998877  7889999999


Q ss_pred             HHhcCCCChHHHHHhh--hhhcCCC-cccccchhHhh
Q 025225          220 KGLLPHPLLRSKVKKD--FEELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       220 ~~~~~~g~~~~a~~~~--~~~~~p~-~~~~~~li~~y  253 (256)
                      ..|...|++++|+...  .-...|+ ...+..+..+|
T Consensus       159 ~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~  195 (217)
T 2pl2_A          159 ELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASAL  195 (217)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence            9999999999998832  2334554 33444444444

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.95  E-value=1.1e-08  Score=84.19  Aligned_cols=216  Identities=10%  Similarity=-0.002  Sum_probs=158.2

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +-+.|+.+.|.+.|+...+...     |..+-..+...++...+     +..|+......+..         ...+..+.
T Consensus        13 ~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l~   78 (359)
T 3ieg_A           13 LLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAA-----LPDLTKVIALKMDF---------TAARLQRG   78 (359)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHH-----HHHHHHHHHhCCCc---------chHHHHHH
Confidence            4568899999999998754332     44444455566777777     88887776543322         24455567


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCC---cHH---H-H------------HHHHHHcCCHHHHHHHHHHHHhcCCCCCC
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKM---DIV---A-V------------LIELERQEETILAVKIFDIIRKQDWYQPD  141 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~---~-l------------i~~~~~~~~~~~a~~~~~~m~~~~~~~p~  141 (256)
                      ..+.+.|+.++|+..+ +...+.  .|   +..   . +            -..+...|++++|.+.+++..+..  +.+
T Consensus        79 ~~~~~~~~~~~A~~~~-~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~  153 (359)
T 3ieg_A           79 HLLLKQGKLDEAEDDF-KKVLKS--NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC--VWD  153 (359)
T ss_dssp             HHHHHHTCHHHHHHHH-HHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTC
T ss_pred             HHHHHcCChHHHHHHH-HHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCc
Confidence            7888999999998544 454433  24   222   1 2            367889999999999999999886  678


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-hhHHH----
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-ELPFR----  216 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-~~t~~----  216 (256)
                      ..++..+...|...|++++|.+.|++..+.. +.+...|..+...|...|++++|.+.|++..+..  |+ ...+.    
T Consensus       154 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~  230 (359)
T 3ieg_A          154 AELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD--QDHKRCFAHYKQ  230 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--ccchHHHHHHHH
Confidence            8999999999999999999999999998753 3467889999999999999999999999988652  33 22222    


Q ss_pred             --------HHHHHhcCCCChHHHHHh--hhhhcCCCc
Q 025225          217 --------ILLKGLLPHPLLRSKVKK--DFEELFPEK  243 (256)
Q Consensus       217 --------~li~~~~~~g~~~~a~~~--~~~~~~p~~  243 (256)
                              .+...+.+.|++++|.+.  ......|+.
T Consensus       231 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~  267 (359)
T 3ieg_A          231 VKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSV  267 (359)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSS
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCc
Confidence                    225668899999999882  223344553

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.93  E-value=1.4e-08  Score=83.51  Aligned_cols=217  Identities=11%  Similarity=0.035  Sum_probs=121.6

Q ss_pred             cccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCC---CCCcccccccc----
Q 025225            5 LFSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRP---RGSLWRGKKLI----   72 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~---~~~~~~~~~~~----   72 (256)
                      .+.+.|+.+.|.+.++...+...     |..+-..+...++...+     +..|+......+   ... .....+.    
T Consensus        46 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~  119 (359)
T 3ieg_A           46 VFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEA-----EDDFKKVLKSNPSEQEEK-EAESQLVKADE  119 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHTSCCCHHHHH-HHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHH-----HHHHHHHHhcCCcccChH-HHHHHHHHHHH
Confidence            35567889999999998754322     55555566666777777     888887765543   110 0000000    


Q ss_pred             chhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           73 GKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        73 ~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      ..........+...|+.++|+..+.+......-.+... .+-..+...|++++|...+++..+..  +.+..+|..+...
T Consensus       120 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~  197 (359)
T 3ieg_A          120 MQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK--SDNTEAFYKISTL  197 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--SCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH
Confidence            00111123556677777777744432222222112222 35666677777777777777777664  5566777777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCH-hhHH------------HHHHHHHHcCChhHHHHHHHHHHhCCCCCCh-----h
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDS-QTYT------------EVIRGFLKDGSPADAMNIYEDMIKSPDPPEE-----L  213 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~------------~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~-----~  213 (256)
                      |...|++++|.+.|++..+.  .|+. ..+.            .+...+.+.|++++|.+.+++..+..  |+.     .
T Consensus       198 ~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~  273 (359)
T 3ieg_A          198 YYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSVAEYTVR  273 (359)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSSHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhh--CccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHHHHH
Confidence            77777777777777776653  1322 2222            12344556666666666666665432  221     1


Q ss_pred             HHHHHHHHhcCCCChHHHHH
Q 025225          214 PFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       214 t~~~li~~~~~~g~~~~a~~  233 (256)
                      .+..+...|.+.|++++|++
T Consensus       274 ~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          274 SKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             HHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHH
Confidence            23334555666666666665

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.92  E-value=5e-09  Score=83.30  Aligned_cols=214  Identities=10%  Similarity=-0.073  Sum_probs=130.0

Q ss_pred             ccccCCchHHHHHHHHHhcCCC---------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS---------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEA   76 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~---------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~   76 (256)
                      +.+.++.+.|++.++.+.+...         |..+-..+...++...+     +..|++.....+..         ...+
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~al~~~~~~---------~~~~   80 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALA-----RNDFSQALAIRPDM---------PEVF   80 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCCCC---------HHHH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHH-----HHHHHHHHHcCCCc---------HHHH
Confidence            4556777888888887765410         44444455556666666     77776655433221         2334


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ..+...+...|+.++|+..+ +...... -.+... .+-..+.+.|++++|...|++..+..   |+...+...+..+..
T Consensus        81 ~~la~~~~~~~~~~~A~~~~-~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~~~  156 (275)
T 1xnf_A           81 NYLGIYLTQAGNFDAAYEAF-DSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD---PNDPFRSLWLYLAEQ  156 (275)
T ss_dssp             HHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHH-HHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC---CCChHHHHHHHHHHH
Confidence            44556677778888877444 3333321 122222 46667777788888888888777664   343344445555566


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC--C-ChhHHHHHHHHhcCCCChHHH
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP--P-EELPFRILLKGLLPHPLLRSK  231 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~--p-~~~t~~~li~~~~~~g~~~~a  231 (256)
                      .|++++|...+++..... .++...+ .+...+...++.++|.+.+.+..+....  | +...|..+...|.+.|++++|
T Consensus       157 ~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  234 (275)
T 1xnf_A          157 KLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSA  234 (275)
T ss_dssp             HHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             hcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHH
Confidence            677888888886665531 2333333 3666666677777777777776654221  1 157788888999999999999


Q ss_pred             HHhhhhhc
Q 025225          232 VKKDFEEL  239 (256)
Q Consensus       232 ~~~~~~~~  239 (256)
                      .+.....+
T Consensus       235 ~~~~~~al  242 (275)
T 1xnf_A          235 TALFKLAV  242 (275)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88444333

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.91  E-value=2.2e-08  Score=77.98  Aligned_cols=174  Identities=13%  Similarity=0.031  Sum_probs=119.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+..+-..+.+.|+.++|+..+ +...... -.+... .+-..+...|++++|.+.|++..+..  ..+..+|..+...|
T Consensus        25 ~~~~~a~~~~~~~~~~~A~~~~-~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~  101 (243)
T 2q7f_A           25 TGGQQMGRGSEFGDYEKAAEAF-TKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD--SSAATAYYGAGNVY  101 (243)
T ss_dssp             -----------------CCTTH-HHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCHHHHHHHH-HHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CcchHHHHHHHHHH
Confidence            4444556678889999998544 4444322 111222 46778889999999999999999886  56889999999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ...|++++|.+.|++..+.. ..+...|..+...|.+.|++++|.+.+++..+.. ..+...+..+...|.+.|++++|.
T Consensus       102 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~  179 (243)
T 2q7f_A          102 VVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEAL  179 (243)
T ss_dssp             HHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999988743 2367889999999999999999999999988652 236778889999999999999998


Q ss_pred             Hhhh--hhcCCC-cccccchhHhh
Q 025225          233 KKDF--EELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       233 ~~~~--~~~~p~-~~~~~~li~~y  253 (256)
                      +...  ....|+ ...+..+..+|
T Consensus       180 ~~~~~~~~~~~~~~~~~~~la~~~  203 (243)
T 2q7f_A          180 SQFAAVTEQDPGHADAFYNAGVTY  203 (243)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcccHHHHHHHHHHH
Confidence            8322  223343 34555555444

>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=98.86  E-value=2.4e-07  Score=64.62  Aligned_cols=127  Identities=13%  Similarity=0.142  Sum_probs=101.5

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCC-CcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLK-MDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      +..+...+...|+.++|...+ +........ +... .+...+...|++++|...|+++.+.+  ..+...|..+...+.
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYY-QKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD--PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCcHHHHHHHH-HHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC--CCchHHHHHHHHHHH
Confidence            344566778899999998544 455443221 1111 46777889999999999999999886  567889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ..|++++|.+.|+++.+.. ..+...+..+...|.+.|++++|.+.|+++.+.
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            9999999999999988743 235788899999999999999999999998764

>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=98.85  E-value=8.3e-08  Score=83.66  Aligned_cols=211  Identities=11%  Similarity=0.026  Sum_probs=156.4

Q ss_pred             ccccCCchHHHHHHHHHhcCCC----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVIL   81 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~   81 (256)
                      +...|+++.|.+.++...+...    |..+-..+...++...+     +..|+......+..         ...+..+..
T Consensus       253 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l~~  318 (537)
T 3fp2_A          253 HFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEF-----FKFFQKAVDLNPEY---------PPTYYHRGQ  318 (537)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHH-----HHHHHHHHHHCTTC---------HHHHHHHHH
T ss_pred             HHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHH-----HHHHHHHhccCCCC---------HHHHHHHHH
Confidence            4567888999999988654322    55555667777877777     88887776543322         334556677


Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNE  160 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~  160 (256)
                      .+...|+.++|+..+.+......-.+... .+-..+...|++++|.+.|++..+..  ..+..+|..+-..|...|++++
T Consensus       319 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~  396 (537)
T 3fp2_A          319 MYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKF--PTLPEVPTFFAEILTDRGDFDT  396 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhCCHHH
Confidence            88899999999865543333322223333 57888889999999999999999885  5677899999999999999999


Q ss_pred             HHHHHHHHHhCC-----CCCCHhhHHHHHHHHHHc----------CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          161 AMQVWESMRKED-----LFPDSQTYTEVIRGFLKD----------GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       161 a~~~~~~m~~~g-----~~p~~~t~~~li~~~~~~----------g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                      |.+.|++..+..     .......+..+-..|.+.          |++++|...|++..+.. +.+...|..+...|.+.
T Consensus       397 A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~  475 (537)
T 3fp2_A          397 AIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQM  475 (537)
T ss_dssp             HHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHh
Confidence            999999987632     111222344445667777          99999999999988753 23567889999999999


Q ss_pred             CChHHHHH
Q 025225          226 PLLRSKVK  233 (256)
Q Consensus       226 g~~~~a~~  233 (256)
                      |++++|.+
T Consensus       476 g~~~~A~~  483 (537)
T 3fp2_A          476 EKIDEAIE  483 (537)
T ss_dssp             TCHHHHHH
T ss_pred             ccHHHHHH
Confidence            99999988

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.85  E-value=5.6e-07  Score=67.21  Aligned_cols=161  Identities=12%  Similarity=-0.023  Sum_probs=126.0

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+..+=..|.+.|+.++|+..+-+......-.++.. .+-..+.+.|++++|...+....+..  .-+...+..+-..+.
T Consensus         7 iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~   84 (184)
T 3vtx_A            7 IYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD--TTSAEAYYILGSANF   84 (184)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--chhHHHHHHHHHHHH
Confidence            344556678889999999965543333222112222 47778889999999999999998886  667888888899999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ..++++.|.+.+++..+.. +-+...+..+-..|.+.|++++|.+.|++..+.. +-+...|..+-..|.+.|++++|++
T Consensus        85 ~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~  162 (184)
T 3vtx_A           85 MIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVK  162 (184)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHH
Confidence            9999999999999987742 2357788899999999999999999999988753 2356788999999999999999999


Q ss_pred             hhhhhc
Q 025225          234 KDFEEL  239 (256)
Q Consensus       234 ~~~~~~  239 (256)
                      ...+.+
T Consensus       163 ~~~~al  168 (184)
T 3vtx_A          163 YFKKAL  168 (184)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444333

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.84  E-value=7e-09  Score=89.86  Aligned_cols=228  Identities=11%  Similarity=-0.017  Sum_probs=166.4

Q ss_pred             cccCCchHHHHHHHHHhc-----C----------CC----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccc
Q 025225            7 SRSKIPILASIVLQNLTK-----N----------PS----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWR   67 (256)
Q Consensus         7 ~~~~~~~~A~~l~~~m~~-----~----------~~----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~   67 (256)
                      .+.|+.+.|.++++.+.+     .          +.    |..+-..+...++...+     +..|++.....+.     
T Consensus       200 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A-----~~~~~~~l~~~~~-----  269 (514)
T 2gw1_A          200 RSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGA-----HEDIKKAIELFPR-----  269 (514)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHH-----HHHHHHHHHHCCC-----
T ss_pred             hhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHhhCcc-----
Confidence            358899999999998766     2          11    44555556667777777     8888777654321     


Q ss_pred             cccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHH
Q 025225           68 GKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIY  145 (256)
Q Consensus        68 ~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y  145 (256)
                           ...+..+...+...|+.++|+..+ +...... -.++.. .+...+...|++++|...|++..+..  ..+..+|
T Consensus       270 -----~~~~~~l~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~  341 (514)
T 2gw1_A          270 -----VNSYIYMALIMADRNDSTEYYNYF-DKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELD--PENIFPY  341 (514)
T ss_dssp             -----HHHHHHHHHHHHTSSCCTTGGGHH-HHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTC--SSCSHHH
T ss_pred             -----HHHHHHHHHHHHHCCCHHHHHHHH-HHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--hhhHHHH
Confidence                 233445567788999999998555 4444332 223333 57788899999999999999999886  5577899


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC-CCC----hhHHHHHHH
Q 025225          146 KDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD-PPE----ELPFRILLK  220 (256)
Q Consensus       146 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~-~p~----~~t~~~li~  220 (256)
                      ..+...|...|++++|.+.|++..+.. +.+...|..+...|.+.|++++|...|+++.+... .|+    ...|..+..
T Consensus       342 ~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~  420 (514)
T 2gw1_A          342 IQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKAT  420 (514)
T ss_dssp             HHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHH
Confidence            999999999999999999999988742 23567899999999999999999999999876421 122    348999999


Q ss_pred             HhcC---CCChHHHHHhh--hhhcCCC-cccccchhHhh
Q 025225          221 GLLP---HPLLRSKVKKD--FEELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       221 ~~~~---~g~~~~a~~~~--~~~~~p~-~~~~~~li~~y  253 (256)
                      .|..   .|++++|.+..  .....|+ ...+..+..+|
T Consensus       421 ~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~  459 (514)
T 2gw1_A          421 LLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMK  459 (514)
T ss_dssp             HHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            9999   99999998822  2233454 33444555444

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.81  E-value=1.9e-07  Score=73.10  Aligned_cols=120  Identities=10%  Similarity=0.011  Sum_probs=64.8

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCC------------------------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDW------------------------YQPDAYIYKDLIIALARTGKMNEAMQVWES  167 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~------------------------~~p~~~~y~~li~~~~~~g~~~~a~~~~~~  167 (256)
                      +-..+.+.|++++|...|++..+...                        ...+...|..+...|...|++++|.+.|++
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  164 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTE  164 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            44555556666666666666555210                        122334455555555666666666666665


Q ss_pred             HHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          168 MRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       168 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ..+.. +.+...|..+...|.+.|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+
T Consensus       165 a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~  228 (258)
T 3uq3_A          165 MIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALE  228 (258)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            55432 1234555566666666666666666666555432 1234555555666666666666655

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.80  E-value=1.2e-07  Score=75.27  Aligned_cols=222  Identities=12%  Similarity=0.009  Sum_probs=157.9

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +-+.|+.+.|++.++...+...     +..+-..+...++...+     +..|++.......+      ......+..+-
T Consensus        13 ~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~a~~~~~~~------~~~~~~~~~lg   81 (272)
T 3u4t_A           13 LFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLA-----QKDIETYFSKVNAT------KAKSADFEYYG   81 (272)
T ss_dssp             HHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHH-----HHHHHHHHTTSCTT------TCCHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHH-----HHHHHHHHhccCch------hHHHHHHHHHH
Confidence            4578899999999998755332     44444566677777777     88888777632111      11233455667


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN  159 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~  159 (256)
                      ..+...|+.++|+..+.+......-.++.. .+-..+...|++++|.+.|++..+..  ..+..+|..+-..+-..++++
T Consensus        82 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~~~~~  159 (272)
T 3u4t_A           82 KILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT--TTDPKVFYELGQAYYYNKEYV  159 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS--CCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC--CCcHHHHHHHHHHHHHHHHHH
Confidence            788899999999865544343333333333 57888899999999999999988775  556777777772444456999


Q ss_pred             HHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCC---hhHHHHHHHHHHhC-CCCCCh------hHHHHHHHHhcCCCCh
Q 025225          160 EAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGS---PADAMNIYEDMIKS-PDPPEE------LPFRILLKGLLPHPLL  228 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~---~~~a~~~~~~M~~~-g~~p~~------~t~~~li~~~~~~g~~  228 (256)
                      +|.+.|++..+.  .|+ ...+..+-..+...|+   .++|...|++..+. .-.|+.      ..|..+-..|.+.|++
T Consensus       160 ~A~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  237 (272)
T 3u4t_A          160 KADSSFVKVLEL--KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDK  237 (272)
T ss_dssp             HHHHHHHHHHHH--STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHh--CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCH
Confidence            999999998874  344 6777778888888888   88899999988754 223442      5778888999999999


Q ss_pred             HHHHH--hhhhhcCCC
Q 025225          229 RSKVK--KDFEELFPE  242 (256)
Q Consensus       229 ~~a~~--~~~~~~~p~  242 (256)
                      ++|.+  ...-.+.|+
T Consensus       238 ~~A~~~~~~al~~~p~  253 (272)
T 3u4t_A          238 VKADAAWKNILALDPT  253 (272)
T ss_dssp             HHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHhcCcc
Confidence            99998  333344554

>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=98.74  E-value=8.3e-07  Score=65.59  Aligned_cols=128  Identities=10%  Similarity=0.111  Sum_probs=102.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+..+...+...|+.++|...+ +...+.. -.+... .+...+...|++++|.+.|++..+..  ..+...+..+...|
T Consensus        44 ~~~~~~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~  120 (186)
T 3as5_A           44 VALHLGIAYVKTGAVDRGTELL-ERSLADAPDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN--PINFNVRFRLGVAL  120 (186)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHH-HHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--cHhHHHHHHHHHHH
Confidence            3445567778999999998554 4443332 112222 46778889999999999999999885  67889999999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ...|++++|.+.|++..+.. ..+...+..+...|.+.|++++|.+.+++..+.
T Consensus       121 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          121 DNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            99999999999999988753 235788999999999999999999999988754

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.73  E-value=7.1e-07  Score=70.66  Aligned_cols=181  Identities=11%  Similarity=-0.004  Sum_probs=128.0

Q ss_pred             CCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHH
Q 025225           37 PKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLI  114 (256)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~  114 (256)
                      ..++.+.+     +..|+++.......+.     -....+..+...+...|+.++|+..+ +...... -.+... .+-.
T Consensus        17 ~~~~~~~A-----~~~~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~A~~~~-~~al~~~~~~~~~~~~la~   85 (275)
T 1xnf_A           17 PTLQQEVI-----LARMEQILASRALTDD-----ERAQLLYERGVLYDSLGLRALARNDF-SQALAIRPDMPEVFNYLGI   85 (275)
T ss_dssp             CCHHHHHH-----HHHHHHHHTSSCCCHH-----HHHHHHHHHHHHHHHTTCHHHHHHHH-HHHHHHCCCCHHHHHHHHH
T ss_pred             ccchHHHH-----HHHHHHHHhcccccCc-----hhHHHHHHHHHHHHHcccHHHHHHHH-HHHHHcCCCcHHHHHHHHH
Confidence            34444455     7788777665321110     11234455667788999999998555 4443322 212222 4777


Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChh
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPA  194 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~  194 (256)
                      .+...|++++|...|++..+..  +.+..+|..+...|...|++++|.+.|+++.+.  .|+...+...+..+...|+++
T Consensus        86 ~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~  161 (275)
T 1xnf_A           86 YLTQAGNFDAAYEAFDSVLELD--PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEK  161 (275)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHH
T ss_pred             HHHHccCHHHHHHHHHHHHhcC--ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHH
Confidence            8889999999999999999875  557889999999999999999999999999873  466666666666677789999


Q ss_pred             HHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          195 DAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       195 ~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      +|...+.+..... .++...+. ++..+...++.++|++.
T Consensus       162 ~A~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~a~~~  199 (275)
T 1xnf_A          162 QAKEVLKQHFEKS-DKEQWGWN-IVEFYLGNISEQTLMER  199 (275)
T ss_dssp             HHHHHHHHHHHHS-CCCSTHHH-HHHHHTTSSCHHHHHHH
T ss_pred             HHHHHHHHHHhcC-CcchHHHH-HHHHHHHhcCHHHHHHH
Confidence            9999998777652 33444444 67777777887888773

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.71  E-value=8.5e-07  Score=69.32  Aligned_cols=152  Identities=12%  Similarity=0.138  Sum_probs=71.4

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCCC----HHHHHHHHHHHHhc
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDW-YQPD----AYIYKDLIIALART  155 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~p~----~~~y~~li~~~~~~  155 (256)
                      ..+...|+.++|+..+.+.............+-..+...|++++|.+.|++..+..+ ..|+    ..+|..+-..|...
T Consensus        13 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~   92 (258)
T 3uq3_A           13 NKFYKARQFDEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKL   92 (258)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhccHHHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHc
Confidence            344455555555533322222223334444455555555555555555555443320 0111    34555555555555


Q ss_pred             CCHHHHHHHHHHHHhCC------------------------CCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC
Q 025225          156 GKMNEAMQVWESMRKED------------------------LFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP  210 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g------------------------~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p  210 (256)
                      |++++|.+.|++..+..                        ..| +...|..+...|.+.|++++|.+.|++..+.. +.
T Consensus        93 ~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~  171 (258)
T 3uq3_A           93 GDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PE  171 (258)
T ss_dssp             TCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             ccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cc
Confidence            55555555555554411                        122 23444555555555555555555555554432 11


Q ss_pred             ChhHHHHHHHHhcCCCChHHHHH
Q 025225          211 EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       211 ~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +...|..+...|.+.|++++|.+
T Consensus       172 ~~~~~~~l~~~~~~~~~~~~A~~  194 (258)
T 3uq3_A          172 DARGYSNRAAALAKLMSFPEAIA  194 (258)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCCHHHHHH
Confidence            34445555555555555555555

>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=98.66  E-value=1.7e-07  Score=81.70  Aligned_cols=226  Identities=14%  Similarity=0.040  Sum_probs=147.7

Q ss_pred             CCchHHHHHHHHHhcCCC------------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHH
Q 025225           10 KIPILASIVLQNLTKNPS------------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEAL   77 (256)
Q Consensus        10 ~~~~~A~~l~~~m~~~~~------------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~   77 (256)
                      ++.+.|.++++.+.+...            +..+-..+...++...+     +..|+......+.          ...+.
T Consensus       216 ~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A-----~~~~~~~~~~~~~----------~~~~~  280 (537)
T 3fp2_A          216 DLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDA-----QVLLQESINLHPT----------PNSYI  280 (537)
T ss_dssp             HHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCCC----------HHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHH-----HHHHHHHHhcCCC----------chHHH
Confidence            366778888887765432            12222233445555666     7777766554321          13344


Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      .+...+...|+.++|+..+.+......-.+... .+-..+...|++++|.+.|++..+..  ..+..+|..+...|...|
T Consensus       281 ~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~g  358 (537)
T 3fp2_A          281 FLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN--PENVYPYIQLACLLYKQG  358 (537)
T ss_dssp             HHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcC
Confidence            556678889999999855543333222222222 47777888999999999999998875  456788999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC-----CCCChhHHHHHHHHhcCC------
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP-----DPPEELPFRILLKGLLPH------  225 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g-----~~p~~~t~~~li~~~~~~------  225 (256)
                      ++++|.+.|++..+.. +.+...|..+-..|.+.|++++|.+.|++..+..     .......+......|.+.      
T Consensus       359 ~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~  437 (537)
T 3fp2_A          359 KFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPT  437 (537)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC---
T ss_pred             CHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccch
Confidence            9999999999988742 2346688889999999999999999999887532     112222344445566666      


Q ss_pred             ----CChHHHHHhhh--hhcCCC-cccccchhHhh
Q 025225          226 ----PLLRSKVKKDF--EELFPE-KHAYDPPEEIF  253 (256)
Q Consensus       226 ----g~~~~a~~~~~--~~~~p~-~~~~~~li~~y  253 (256)
                          |++++|.....  ....|+ ...|..+..+|
T Consensus       438 ~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~  472 (537)
T 3fp2_A          438 QLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLK  472 (537)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence                88898888222  333454 34455555544

>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=98.58  E-value=3.4e-06  Score=67.12  Aligned_cols=200  Identities=8%  Similarity=-0.093  Sum_probs=145.6

Q ss_pred             ccccCCchHHHHHHHHHhcCCC---ccccccccCC----CCCCCCcccCcccccccccccCCCCCCccccccccchhHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS---KNFSFLAFKP----KSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALF   78 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~---~~~ll~a~~~----~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~   78 (256)
                      +-+.++.+.|.+.|+...+.+.   +..+-..+..    .++...+     +..|++....+           ....+..
T Consensus        16 ~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A-----~~~~~~a~~~~-----------~~~a~~~   79 (273)
T 1ouv_A           16 SYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKA-----ASFYAKACDLN-----------YSNGCHL   79 (273)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHH-----HHHHHHHHHTT-----------CHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcCCCHHHH-----HHHHHHHHHCC-----------CHHHHHH
Confidence            4456889999999998776554   2222223333    5555555     77777665442           1223333


Q ss_pred             HHHHhhc----CCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHH----cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           79 VILGLKR----FKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELER----QEETILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        79 ~i~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      +-..|..    .++.++|+. +++.....+. +... .+=..+..    .+++++|.+.|++..+.+    +...+..+-
T Consensus        80 lg~~~~~g~~~~~~~~~A~~-~~~~a~~~~~-~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~----~~~a~~~lg  153 (273)
T 1ouv_A           80 LGNLYYSGQGVSQNTNKALQ-YYSKACDLKY-AEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN----DGDGCTILG  153 (273)
T ss_dssp             HHHHHHHTSSSCCCHHHHHH-HHHHHHHTTC-HHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHH
T ss_pred             HHHHHhCCCCcccCHHHHHH-HHHHHHHcCC-ccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC----cHHHHHHHH
Confidence            4455666    899999985 4455555552 3322 46666777    899999999999998876    567788888


Q ss_pred             HHHHh----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCCCCChhHHHHHHHH
Q 025225          150 IALAR----TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPDPPEELPFRILLKG  221 (256)
Q Consensus       150 ~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~  221 (256)
                      ..|..    .+++++|.+.|++..+.+   +...+..+-..|.+    .+++++|.+.|++..+.+.   ...+..+-..
T Consensus       154 ~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~---~~a~~~l~~~  227 (273)
T 1ouv_A          154 SLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN---GGGCFNLGAM  227 (273)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHH
T ss_pred             HHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC---HHHHHHHHHH
Confidence            88888    899999999999988863   56788888888999    9999999999999888753   5677777788


Q ss_pred             hcC----CCChHHHHH
Q 025225          222 LLP----HPLLRSKVK  233 (256)
Q Consensus       222 ~~~----~g~~~~a~~  233 (256)
                      |.+    .+++++|.+
T Consensus       228 ~~~g~~~~~~~~~A~~  243 (273)
T 1ouv_A          228 QYNGEGVTRNEKQAIE  243 (273)
T ss_dssp             HHTTSSSSCCSTTHHH
T ss_pred             HHcCCCcccCHHHHHH
Confidence            887    889888888

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.56  E-value=6.3e-06  Score=67.08  Aligned_cols=180  Identities=12%  Similarity=-0.034  Sum_probs=130.7

Q ss_pred             cccccccccC-CCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCc-HH-HHHHHHHHcCCHHHH
Q 025225           50 ILGLRQYHDG-RPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMD-IV-AVLIELERQEETILA  125 (256)
Q Consensus        50 ~~~~~~m~~~-~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~-~~-~li~~~~~~~~~~~a  125 (256)
                      ..+|++.... .+..         ...|......+.+.|+.++|...+ +...+.. -.++ .. .+...+.+.|++++|
T Consensus        84 ~~~~~rAl~~~~p~~---------~~~~~~~~~~~~~~~~~~~A~~~~-~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A  153 (308)
T 2ond_A           84 ANIYERAISTLLKKN---------MLLYFAYADYEESRMKYEKVHSIY-NRLLAIEDIDPTLVYIQYMKFARRAEGIKSG  153 (308)
T ss_dssp             HHHHHHHHTTTTTTC---------HHHHHHHHHHHHHTTCHHHHHHHH-HHHHTSSSSCTHHHHHHHHHHHHHHHCHHHH
T ss_pred             HHHHHHHHHHhCccc---------HHHHHHHHHHHHhcCCHHHHHHHH-HHHHhccccCccHHHHHHHHHHHHhcCHHHH
Confidence            8888777663 3222         235566677778899999998555 4554422 2233 22 577778889999999


Q ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHHHHH-hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          126 VKIFDIIRKQDWYQPDAYIYKDLIIALA-RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       126 ~~~~~~m~~~~~~~p~~~~y~~li~~~~-~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      ..+|++..+..  .++...|........ ..|+.++|.++|++..+.. +-+...|..++..+.+.|++++|..+|++..
T Consensus       154 ~~~~~~a~~~~--p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al  230 (308)
T 2ond_A          154 RMIFKKAREDA--RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVL  230 (308)
T ss_dssp             HHHHHHHHTST--TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC--CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            99999999876  445555654433322 3699999999999987742 1267889999999999999999999999999


Q ss_pred             hCC-CCC--ChhHHHHHHHHhcCCCChHHHHHhhh--hhcCCC
Q 025225          205 KSP-DPP--EELPFRILLKGLLPHPLLRSKVKKDF--EELFPE  242 (256)
Q Consensus       205 ~~g-~~p--~~~t~~~li~~~~~~g~~~~a~~~~~--~~~~p~  242 (256)
                      +.. +.|  +...|..++..+.+.|+.+++.....  ....|+
T Consensus       231 ~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~~p~  273 (308)
T 2ond_A          231 TSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFRE  273 (308)
T ss_dssp             HSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTT
T ss_pred             hccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccc
Confidence            873 566  46688889999999999999887332  344565

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.56  E-value=1.2e-06  Score=71.33  Aligned_cols=177  Identities=11%  Similarity=-0.049  Sum_probs=131.1

Q ss_pred             hHHHHHHHHHhcC-CC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcC
Q 025225           13 ILASIVLQNLTKN-PS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRF   86 (256)
Q Consensus        13 ~~A~~l~~~m~~~-~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   86 (256)
                      +.|.++|+...+. ..     |..+...+.+.++.+.+     ..+|++.....+..        ....|......+.+.
T Consensus        81 ~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A-----~~~~~~al~~~p~~--------~~~~~~~~~~~~~~~  147 (308)
T 2ond_A           81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKV-----HSIYNRLLAIEDID--------PTLVYIQYMKFARRA  147 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHTSSSSC--------THHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHH-----HHHHHHHHhccccC--------ccHHHHHHHHHHHHh
Confidence            8999999987652 22     55666666667777777     89998887643321        011456667777889


Q ss_pred             CCcHHHHHHHHHHHhhccCCCcHHH-HHHHHH---HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 025225           87 KDDEEKLQKFIKTHVLRLLKMDIVA-VLIELE---RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAM  162 (256)
Q Consensus        87 ~~~~~a~~~~~~~~~~~~~~~~~~~-li~~~~---~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~  162 (256)
                      |+.++|...+ +...+..- ++... +-.+..   ..|+.++|..+|+...+..  .-+...|..++..+.+.|++++|.
T Consensus       148 ~~~~~A~~~~-~~a~~~~p-~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~A~  223 (308)
T 2ond_A          148 EGIKSGRMIF-KKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTR  223 (308)
T ss_dssp             HCHHHHHHHH-HHHHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHH
T ss_pred             cCHHHHHHHH-HHHHhcCC-CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHCCCHHHHH
Confidence            9999998544 45444321 12121 111222   3699999999999988774  558899999999999999999999


Q ss_pred             HHHHHHHhCC-CCC--CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          163 QVWESMRKED-LFP--DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       163 ~~~~~m~~~g-~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      .+|++..... +.|  ....|..++..+.+.|+.++|..+++++.+.
T Consensus       224 ~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          224 VLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            9999999863 555  4678999999999999999999999998875

>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=98.53  E-value=5.5e-06  Score=75.53  Aligned_cols=150  Identities=12%  Similarity=0.042  Sum_probs=123.2

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLII  150 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~  150 (256)
                      .+..+-..|.+.|+.++|+..+ +...+  +.|+..    .+=.++.+.|++++|++.|++..+..  .-+...|+.+-.
T Consensus        11 al~nLG~~~~~~G~~~eAi~~~-~kAl~--l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~--P~~~~a~~nLg~   85 (723)
T 4gyw_A           11 SLNNLANIKREQGNIEEAVRLY-RKALE--VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS--PTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHH--HCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHH-HHHHH--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHH
Confidence            3444557788999999998655 44433  234432    47778889999999999999998886  557889999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCCh
Q 025225          151 ALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPLL  228 (256)
Q Consensus       151 ~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~  228 (256)
                      .|...|++++|.+.|++..+.  .| +...|+.+-..|.+.|++++|.+.|++..+.  .| +...|..+...|...|++
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~~  161 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCDW  161 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhcccH
Confidence            999999999999999998873  35 4688999999999999999999999998875  33 467888999999999999


Q ss_pred             HHHHH
Q 025225          229 RSKVK  233 (256)
Q Consensus       229 ~~a~~  233 (256)
                      ++|.+
T Consensus       162 ~~A~~  166 (723)
T 4gyw_A          162 TDYDE  166 (723)
T ss_dssp             TTHHH
T ss_pred             HHHHH
Confidence            88877

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.52  E-value=6.7e-07  Score=77.61  Aligned_cols=199  Identities=11%  Similarity=-0.059  Sum_probs=134.1

Q ss_pred             hHHHHHHHHHhcCCC-----ccccccccCCCCCC-CCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhcC
Q 025225           13 ILASIVLQNLTKNPS-----KNFSFLAFKPKSPI-VDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRF   86 (256)
Q Consensus        13 ~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~-~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   86 (256)
                      +.|++.+++......     |..+=..+...++. ..+     +..|++.....+..         ...+..+-..|.+.
T Consensus        85 ~~al~~l~~~~~~~~~~a~~~~~lg~~~~~~g~~~~~A-----~~~~~~al~~~p~~---------~~a~~~lg~~~~~~  150 (474)
T 4abn_A           85 EKTLQQMEEVLGSAQVEAQALMLKGKALNVTPDYSPEA-----EVLLSKAVKLEPEL---------VEAWNQLGEVYWKK  150 (474)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHTSSSSCCHHH-----HHHHHHHHHHCTTC---------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCchhHHHHHHHHHHHHhccccHHHH-----HHHHHHHHhhCCCC---------HHHHHHHHHHHHHc
Confidence            344555555443332     33333445556666 666     77777665443222         23455556677888


Q ss_pred             CCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHc---------CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           87 KDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQ---------EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        87 ~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~---------~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      |+.++|...+ +...+..  |+..   .+-..+...         |++++|.+.|++..+..  .-+...|..+-.+|..
T Consensus       151 g~~~~A~~~~-~~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~  225 (474)
T 4abn_A          151 GDVTSAHTCF-SGALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD--VLDGRSWYILGNAYLS  225 (474)
T ss_dssp             TCHHHHHHHH-HHHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHH-HHHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHH
Confidence            8888887544 4444332  4432   255556667         88888888888888775  5567888888888888


Q ss_pred             c--------CCHHHHHHHHHHHHhCCCCC----CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          155 T--------GKMNEAMQVWESMRKEDLFP----DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       155 ~--------g~~~~a~~~~~~m~~~g~~p----~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      .        |++++|.+.|++..+.  .|    +...|..+-..|.+.|++++|.+.|++..+.. .-+...+..+-..+
T Consensus       226 ~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~  302 (474)
T 4abn_A          226 LYFNTGQNPKISQQALSAYAQAEKV--DRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLL  302 (474)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHH--CGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHhhccccchHHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            8        8888888888888773  35    67788888888888888989988888877652 12445677777778


Q ss_pred             cCCCChHHHHH
Q 025225          223 LPHPLLRSKVK  233 (256)
Q Consensus       223 ~~~g~~~~a~~  233 (256)
                      ...|++++|++
T Consensus       303 ~~lg~~~eAi~  313 (474)
T 4abn_A          303 EFLSRLTSLLE  313 (474)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            88888888776

>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=98.52  E-value=1.6e-06  Score=68.55  Aligned_cols=160  Identities=13%  Similarity=0.089  Sum_probs=117.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhc------cCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc-----CCC-
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLR------LLKMDIV----AVLIELERQEETILAVKIFDIIRKQ-----DWY-  138 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~-----~~~-  138 (256)
                      .+..+-..+...|+.++|+..+ +.....      +-.|...    .+-..+...|++++|.+.|.+..+.     +.- 
T Consensus        45 ~~~~l~~~~~~~g~~~~A~~~~-~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  123 (283)
T 3edt_B           45 MLNILALVYRDQNKYKEAAHLL-NDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFH  123 (283)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHcccHHHHHHHH-HHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCC
Confidence            4445567788999999998554 444332      2223322    3777888999999999999988765     101 


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKE------DLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----  206 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----  206 (256)
                      .....+|..+-..|...|++++|.+.|++..+.      +-.| ...++..+-..|.+.|++++|.++|++..+.     
T Consensus       124 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~  203 (283)
T 3edt_B          124 PDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKE  203 (283)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhc
Confidence            234678889999999999999999999998764      1133 3567889999999999999999999987752     


Q ss_pred             -------------------------------------------CCCCChhHHHHHHHHhcCCCChHHHHHhh
Q 025225          207 -------------------------------------------PDPPEELPFRILLKGLLPHPLLRSKVKKD  235 (256)
Q Consensus       207 -------------------------------------------g~~p~~~t~~~li~~~~~~g~~~~a~~~~  235 (256)
                                                                 .......++..+...|.+.|++++|.+..
T Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  275 (283)
T 3edt_B          204 FGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLE  275 (283)
T ss_dssp             SSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence                                                       11123346777888888999999888743

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.49  E-value=3.9e-06  Score=62.55  Aligned_cols=129  Identities=12%  Similarity=0.072  Sum_probs=102.1

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+..+-..|.+.|+.++++..+........-.+... .+-..+...++++.|...+.+..+..  +-+...+..+-..|.
T Consensus        41 ~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~--~~~~~~~~~lg~~~~  118 (184)
T 3vtx_A           41 TLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMIDEKQAAIDALQRAIALN--TVYADAYYKLGLVYD  118 (184)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHH
Confidence            444556778899999999865543333322222222 35567778999999999999998885  667889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      +.|++++|.+.|++..+.. +.+...|..+-..|.+.|++++|.+.|++..+.
T Consensus       119 ~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          119 SMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence            9999999999999988742 135678999999999999999999999998875

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.48  E-value=1.9e-06  Score=69.26  Aligned_cols=159  Identities=10%  Similarity=0.055  Sum_probs=117.5

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhc------cCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc------CCC
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLR------LLKMDIV----AVLIELERQEETILAVKIFDIIRKQ------DWY  138 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~------~~~  138 (256)
                      .+..+...+...|+.++|...+ +.....      +-.|...    .+-..+...|++++|...|++..+.      +..
T Consensus        71 ~~~~la~~~~~~g~~~~A~~~~-~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~  149 (311)
T 3nf1_A           71 MLNILALVYRDQNKYKDAANLL-NDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDH  149 (311)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHH-HHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCC
Confidence            3445567788899999998544 444332      2223222    4777888999999999999988765      211


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKE------DLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----  206 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----  206 (256)
                      .....++..+-..|...|++++|.+.|++..+.      +-.|+ ..++..+...|.+.|++++|.+.|++..+.     
T Consensus       150 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  229 (311)
T 3nf1_A          150 PDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHERE  229 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhc
Confidence            234567888899999999999999999998764      22333 467889999999999999999999988752     


Q ss_pred             -------------------------------------------CCCCChhHHHHHHHHhcCCCChHHHHHh
Q 025225          207 -------------------------------------------PDPPEELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       207 -------------------------------------------g~~p~~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                                                                 .-..+..++..+...|.+.|++++|.+.
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  300 (311)
T 3nf1_A          230 FGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETL  300 (311)
T ss_dssp             HC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             CCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHH
Confidence                                                       1122446677888899999999999883

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.48  E-value=2.1e-06  Score=69.04  Aligned_cols=158  Identities=12%  Similarity=0.068  Sum_probs=119.0

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhc----c--CCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc------CCC
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLR----L--LKMDIV----AVLIELERQEETILAVKIFDIIRKQ------DWY  138 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~----~--~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~------~~~  138 (256)
                      .+..+...+...|+.++|+..+ +.....    +  -.|...    .+-..+...|++++|...+++..+.      +..
T Consensus        29 ~~~~l~~~~~~~g~~~~A~~~~-~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  107 (311)
T 3nf1_A           29 TLHNLVIQYASQGRYEVAVPLC-KQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDH  107 (311)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHH-HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            4455667888999999998544 444331    1  122222    3777788999999999999988765      211


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKE------DLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----  206 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----  206 (256)
                      .....+|..+...|...|++++|.+.|++..+.      +-.| ....+..+-..|...|++++|.++|++..+.     
T Consensus       108 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~  187 (311)
T 3nf1_A          108 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKL  187 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence            334678899999999999999999999998763      2223 3567888999999999999999999998764     


Q ss_pred             -CCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          207 -PDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       207 -g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                       +-.| ...++..+...|...|++++|.+
T Consensus       188 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~  216 (311)
T 3nf1_A          188 GPDDPNVAKTKNNLASCYLKQGKFKQAET  216 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence             2233 34578889999999999999988

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.47  E-value=6.5e-06  Score=56.45  Aligned_cols=93  Identities=15%  Similarity=0.230  Sum_probs=77.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+...+...|++++|.+.|++..+..  ..+..++..+...|.+.|++++|...|+++.+.. ..+..++..+...|.+.
T Consensus        14 ~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~   90 (125)
T 1na0_A           14 NLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQ   90 (125)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHh
Confidence            36667788899999999999888775  5678888888999999999999999999887742 23667888888889999


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|...|++..+.
T Consensus        91 ~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           91 GDYDEAIEYYQKALEL  106 (125)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHh
Confidence            9999999999988765

>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=98.46  E-value=3.6e-05  Score=61.06  Aligned_cols=105  Identities=10%  Similarity=-0.034  Sum_probs=51.4

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----c
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----D  190 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~  190 (256)
                      .+++++|.+.|++..+.+    +...+..+-..|..    .+++++|.+.|++..+.+   +...+..+-..|.+    .
T Consensus        91 ~~~~~~A~~~~~~a~~~~----~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~  163 (273)
T 1ouv_A           91 SQNTNKALQYYSKACDLK----YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTP  163 (273)
T ss_dssp             CCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSC
T ss_pred             ccCHHHHHHHHHHHHHcC----CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCC
Confidence            455555555555554443    34445555555555    555555555555554432   33444444444444    4


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC----CCChHHHHH
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP----HPLLRSKVK  233 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~  233 (256)
                      +++++|.+.|++..+.+   +...+..+-..|..    .+++++|++
T Consensus       164 ~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~  207 (273)
T 1ouv_A          164 KDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALA  207 (273)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            55555555555544442   23444444444444    555555555

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.45  E-value=3e-05  Score=61.11  Aligned_cols=151  Identities=14%  Similarity=0.042  Sum_probs=96.7

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCC--CHHHHHHHHHHHHhcC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQP--DAYIYKDLIIALARTG  156 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p--~~~~y~~li~~~~~~g  156 (256)
                      -..+.+.|+.++|+..+.+......-.+... .+-..+...|++++|.+.|++..+.+ -.|  ...+|..+-..|...|
T Consensus        10 a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~lg~~~~~~~   88 (272)
T 3u4t_A           10 ADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKV-NATKAKSADFEYYGKILMKKG   88 (272)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTS-CTTTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHcc
Confidence            4556677888888754433333222223222 46667778888888888888877643 222  2345777888888888


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++++|.+.|++..+.. +.+...|..+-..|.+.|++++|.+.|++..+.. ..+...|..+-..+...+++++|.+
T Consensus        89 ~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  163 (272)
T 3u4t_A           89 QDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKADS  163 (272)
T ss_dssp             CHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888888777632 1245677788888888888888888888776651 2234455555513333447777777

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.45  E-value=5.6e-06  Score=71.76  Aligned_cols=165  Identities=10%  Similarity=-0.024  Sum_probs=127.4

Q ss_pred             hHHHHHHHhhcCCCc-HHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDD-EEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+..+-..+...|+. ++|+..+.+......-.++.. .+-..|.+.|++++|.+.|++..+..   |+...|..+-..|
T Consensus       104 ~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~---p~~~~~~~lg~~~  180 (474)
T 4abn_A          104 ALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC---KNKVSLQNLSMVL  180 (474)
T ss_dssp             HHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC---CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC---CCHHHHHHHHHHH
Confidence            344445677889999 999865543333322222222 47778889999999999999998764   7789999999999


Q ss_pred             Hhc---------CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc--------CChhHHHHHHHHHHhCCCC--CChh
Q 025225          153 ART---------GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD--------GSPADAMNIYEDMIKSPDP--PEEL  213 (256)
Q Consensus       153 ~~~---------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~--------g~~~~a~~~~~~M~~~g~~--p~~~  213 (256)
                      ...         |++++|.+.|++..+.. .-+...|..+-..|...        |++++|.+.|++..+..-.  -+..
T Consensus       181 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~  259 (474)
T 4abn_A          181 RQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPD  259 (474)
T ss_dssp             TTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHH
T ss_pred             HHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHH
Confidence            999         99999999999988742 12578899999999998        9999999999998875210  3788


Q ss_pred             HHHHHHHHhcCCCChHHHHHh--hhhhcCCCc
Q 025225          214 PFRILLKGLLPHPLLRSKVKK--DFEELFPEK  243 (256)
Q Consensus       214 t~~~li~~~~~~g~~~~a~~~--~~~~~~p~~  243 (256)
                      .|..+-..|...|++++|.+.  ....+.|+.
T Consensus       260 ~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~  291 (474)
T 4abn_A          260 LHLNRATLHKYEESYGEALEGFSQAAALDPAW  291 (474)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence            899999999999999999993  333445653

>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=98.37  E-value=2.9e-05  Score=59.83  Aligned_cols=146  Identities=14%  Similarity=0.015  Sum_probs=111.8

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      +...-..+.+.|+.++|+..+ +......-.++..   .+-.++...|++++|.+.|++..+..  +-+..+|..+-..|
T Consensus        10 ~~~~g~~~~~~~~~~~A~~~~-~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~   86 (228)
T 4i17_A           10 LKNEGNDALNAKNYAVAFEKY-SEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN--YNLANAYIGKSAAY   86 (228)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHH-HHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--CSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHH-HHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC--cchHHHHHHHHHHH
Confidence            344456678899999998555 4444433223333   36667788999999999999999875  45778899999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCC-H-------hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC---hhHHHHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPD-S-------QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE---ELPFRILLKG  221 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~-~-------~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~---~~t~~~li~~  221 (256)
                      ...|++++|.+.|++..+.  .|+ .       ..|..+=..+.+.|++++|.+.|++..+.  .|+   ...|..+-..
T Consensus        87 ~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l~~~  162 (228)
T 4i17_A           87 RDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSLGVL  162 (228)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHHHHH
T ss_pred             HHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHHHHH
Confidence            9999999999999998874  344 3       45677777788899999999999998876  454   4667777777


Q ss_pred             hcCCCCh
Q 025225          222 LLPHPLL  228 (256)
Q Consensus       222 ~~~~g~~  228 (256)
                      |...|..
T Consensus       163 ~~~~~~~  169 (228)
T 4i17_A          163 FYNNGAD  169 (228)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7777766

>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=98.30  E-value=1.6e-05  Score=72.51  Aligned_cols=136  Identities=15%  Similarity=0.107  Sum_probs=112.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~  190 (256)
                      +=..+.+.|++++|++.|++..+..  .-+..+|+.+-..|.+.|++++|.+.|++..+.  .|+ ...|+.+-..|.+.
T Consensus        15 LG~~~~~~G~~~eAi~~~~kAl~l~--P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~~l~~~   90 (723)
T 4gyw_A           15 LANIKREQGNIEEAVRLYRKALEVF--PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEM   90 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHc
Confidence            6667888999999999999998885  557899999999999999999999999998874  454 68899999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCChHHHHHh--hhhhcCCCc-ccccchhHhh
Q 025225          191 GSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPLLRSKVKK--DFEELFPEK-HAYDPPEEIF  253 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~--~~~~~~p~~-~~~~~li~~y  253 (256)
                      |++++|.+.|++..+.  .| +...|+.+-..|.+.|++++|++.  ..-.+.|+. ..|..+..+|
T Consensus        91 g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l  155 (723)
T 4gyw_A           91 QDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCL  155 (723)
T ss_dssp             TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHH
Confidence            9999999999998865  23 467899999999999999999993  334455653 3444454444

>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=98.27  E-value=2.3e-06  Score=72.16  Aligned_cols=198  Identities=11%  Similarity=0.081  Sum_probs=124.9

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCC-CCCcccCcccccccccccCCCCCCccccccccchhHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSP-IVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFV   79 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~-~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~   79 (256)
                      +.+.|+.+.|++.++...+..-     |+.+-..+...++ ...+     +..|++.....+..         ...|..+
T Consensus       107 ~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eA-----l~~~~~al~l~P~~---------~~a~~~~  172 (382)
T 2h6f_A          107 LQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEE-----MNYITAIIEEQPKN---------YQVWHHR  172 (382)
T ss_dssp             HHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHH-----HHHHHHHHHHCTTC---------HHHHHHH
T ss_pred             HHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHH-----HHHHHHHHHHCCCC---------HHHHHHH
Confidence            3456778888888887543221     4444444555554 6666     77777666544332         2334444


Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh-
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR-  154 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~-  154 (256)
                      -..+.+.|+.++|+..+ +.....  .|+..    .+-.++.+.|++++|+..|+++.+..  .-+...|+.+-..|.+ 
T Consensus       173 g~~~~~~g~~~eAl~~~-~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~--P~~~~a~~~lg~~l~~l  247 (382)
T 2h6f_A          173 RVLVEWLRDPSQELEFI-ADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFVISNT  247 (382)
T ss_dssp             HHHHHHHTCCTTHHHHH-HHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHccCHHHHHHHH-HHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHh
Confidence            45566778888887444 444332  23222    35556667788888888888888776  5577888888888888 


Q ss_pred             cCCHHHH-----HHHHHHHHhCCCCC-CHhhHHHHHHHHHHcC--ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCC
Q 025225          155 TGKMNEA-----MQVWESMRKEDLFP-DSQTYTEVIRGFLKDG--SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHP  226 (256)
Q Consensus       155 ~g~~~~a-----~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g--~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g  226 (256)
                      .|..++|     .+.|++..+.  .| +...|+.+-..|.+.|  +.++|.+.+.++  ..-..+...+..+...|.+.|
T Consensus       248 ~~~~~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~--~~~p~~~~al~~La~~~~~~~  323 (382)
T 2h6f_A          248 TGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL--QPSHSSPYLIAFLVDIYEDML  323 (382)
T ss_dssp             TCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH--TTTCCCHHHHHHHHHHHHHHH
T ss_pred             cCcchHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHHHHh--ccCCCCHHHHHHHHHHHHHHh
Confidence            5554666     4667766652  34 4567777777777777  578888888777  222345566777777777653

>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=98.26  E-value=2.5e-05  Score=69.09  Aligned_cols=118  Identities=10%  Similarity=-0.107  Sum_probs=63.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +-..+...|++++|.+.|++..+..  .-+...|..+-..|...|++++|.+.|++..+.. ..+...|..+-..|.+.|
T Consensus        29 lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g  105 (568)
T 2vsy_A           29 LADAELGMGDTTAGEMAVQRGLALH--PGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAG  105 (568)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHTTS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcC
Confidence            4444455566666666666555543  3345555555556666666666666666555421 113445555555566666


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC---CChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH---PLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~---g~~~~a~~  233 (256)
                      ++++|.+.|++..+.. .-+...+..+...+...   |+.++|.+
T Consensus       106 ~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A          106 QAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHH
Confidence            6666666666555431 11334455555555555   55555555

>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=98.24  E-value=2.3e-06  Score=67.66  Aligned_cols=193  Identities=10%  Similarity=-0.005  Sum_probs=126.3

Q ss_pred             cccCCchHHHHHHHHHhc-------CC-C-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccc
Q 025225            7 SRSKIPILASIVLQNLTK-------NP-S-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIG   73 (256)
Q Consensus         7 ~~~~~~~~A~~l~~~m~~-------~~-~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~   73 (256)
                      ...|+++.|.+++++..+       .. .     +..+-..+...++...+     +..|++.......... .......
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~~~~~~-~~~~~~~   85 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEA-----AHLLNDALAIREKTLG-KDHPAVA   85 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHHHHHTC-TTCHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHH-----HHHHHHHHHHHHHHcC-CcchHHH
Confidence            445667777666665332       22 1     55555566667777777     7777665533100000 0000112


Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhc------cCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc-----CCC
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLR------LLKMDIV----AVLIELERQEETILAVKIFDIIRKQ-----DWY  138 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~-----~~~  138 (256)
                      ..+..+-..+...|+.++|+..+. .....      .-.|+..    .+-..+...|++++|...|++..+.     +.-
T Consensus        86 ~~~~~l~~~~~~~g~~~~A~~~~~-~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  164 (283)
T 3edt_B           86 ATLNNLAVLYGKRGKYKEAEPLCK-RALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPD  164 (283)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHH-HHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHH-HHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCC
Confidence            345556678889999999985553 43322      1123322    3677788999999999999998765     101


Q ss_pred             CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----------------------------------------------
Q 025225          139 QP-DAYIYKDLIIALARTGKMNEAMQVWESMRKE----------------------------------------------  171 (256)
Q Consensus       139 ~p-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----------------------------------------------  171 (256)
                      .| ...++..+-..|...|++++|.+.|++..+.                                              
T Consensus       165 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (283)
T 3edt_B          165 DPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKAC  244 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CC
T ss_pred             CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhc
Confidence            22 3578889999999999999999999988752                                              


Q ss_pred             --CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          172 --DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       172 --g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                        ....+..++..+-..|.+.|++++|..+|++..+.
T Consensus       245 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          245 KVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence              01112456888999999999999999999987653

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.24  E-value=5.8e-05  Score=60.88  Aligned_cols=155  Identities=14%  Similarity=-0.022  Sum_probs=111.5

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhh---ccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCC--CC--CHHHHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVL---RLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWY--QP--DAYIYKDL  148 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~--~p--~~~~y~~l  148 (256)
                      ...|...|+.++|+..+.+....   .+-.++..    .+-..|.+.|++++|+..|++..+...-  .+  -..+|+.+
T Consensus        44 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~l  123 (292)
T 1qqe_A           44 ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFEL  123 (292)
T ss_dssp             HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45677899999998655433322   22222211    3677788999999999999977644200  11  14688889


Q ss_pred             HHHHHhc-CCHHHHHHHHHHHHhC----CCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChh------HHH
Q 025225          149 IIALART-GKMNEAMQVWESMRKE----DLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEEL------PFR  216 (256)
Q Consensus       149 i~~~~~~-g~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~------t~~  216 (256)
                      -..|... |++++|.+.|++..+.    +-.+. ..+|+.+-..|.+.|++++|.+.|++..+........      .|.
T Consensus       124 g~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  203 (292)
T 1qqe_A          124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFL  203 (292)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHH
T ss_pred             HHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Confidence            9999996 9999999999988762    11001 3578899999999999999999999998764332221      567


Q ss_pred             HHHHHhcCCCChHHHHHh
Q 025225          217 ILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       217 ~li~~~~~~g~~~~a~~~  234 (256)
                      .+..++...|++++|...
T Consensus       204 ~lg~~~~~~g~~~~A~~~  221 (292)
T 1qqe_A          204 KKGLCQLAATDAVAAART  221 (292)
T ss_dssp             HHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHH
Confidence            778889999999999983

>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=98.24  E-value=4e-05  Score=58.23  Aligned_cols=126  Identities=13%  Similarity=-0.072  Sum_probs=98.0

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ..-..+...|+.++|+..+ +..    +.|+..   .+-..+.+.|++++|...|++..+..  ..+...|..+-..|..
T Consensus        11 ~~g~~~~~~~~~~~A~~~~-~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~lg~~~~~   83 (213)
T 1hh8_A           11 NEGVLAADKKDWKGALDAF-SAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD--KHLAVAYFQRGMLYYQ   83 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHH-HTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHH-HHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHH
Confidence            3455677889999998544 333    344443   46777888999999999999988875  5678899999999999


Q ss_pred             cCCHHHHHHHHHHHHhCCC--------------CC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCCh
Q 025225          155 TGKMNEAMQVWESMRKEDL--------------FP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEE  212 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~--------------~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~  212 (256)
                      .|++++|.+.|++..+..-              .| +...|..+-..|.+.|++++|.+.|++..+.  .|+.
T Consensus        84 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~  154 (213)
T 1hh8_A           84 TEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM--KSEP  154 (213)
T ss_dssp             TTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCSG
T ss_pred             cccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc--Cccc
Confidence            9999999999999887421              11 1267888888999999999999999998876  4665

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.23  E-value=6.1e-05  Score=52.78  Aligned_cols=97  Identities=15%  Similarity=0.167  Sum_probs=80.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      .=+.+.+.|++++|++.|++..+..  +.+..+|..+-.+|.+.|++++|.+.|++..+.. +.+...|..+-..|...|
T Consensus        19 ~G~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~   95 (126)
T 4gco_A           19 KGNEYFKKGDYPTAMRHYNEAVKRD--PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVAMR   95 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHHCC
Confidence            4456788999999999999988886  6688899999999999999999999999888742 124678888889999999


Q ss_pred             ChhHHHHHHHHHHhCCCCCChh
Q 025225          192 SPADAMNIYEDMIKSPDPPEEL  213 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~  213 (256)
                      ++++|.+.|++..+.  .|+..
T Consensus        96 ~~~~A~~~~~~al~l--~P~~~  115 (126)
T 4gco_A           96 EWSKAQRAYEDALQV--DPSNE  115 (126)
T ss_dssp             CHHHHHHHHHHHHHH--CTTCH
T ss_pred             CHHHHHHHHHHHHHH--CcCCH
Confidence            999999999988765  35433

>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=98.23  E-value=1.3e-05  Score=58.01  Aligned_cols=135  Identities=11%  Similarity=-0.016  Sum_probs=99.5

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN  159 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~  159 (256)
                      ...|+.++|+..+. ...  ...|+..    .+=..|.+.|++++|.+.|++..+..  +-+..+|..+-..|.+.|+++
T Consensus         8 ~~~~~~e~ai~~~~-~a~--~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~   82 (150)
T 4ga2_A            8 RSKADVERYIASVQ-GST--PSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ--ERDPKAHRFLGLLYELEENTD   82 (150)
T ss_dssp             CCHHHHHHHHHHHH-HHS--CSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHcChHHHHHHHHH-Hhc--ccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCchH
Confidence            44566777775443 221  1223222    46677889999999999999999886  568899999999999999999


Q ss_pred             HHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHH-HHHHHhCCCCC-ChhHHHHHHHHhcCCCC
Q 025225          160 EAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNI-YEDMIKSPDPP-EELPFRILLKGLLPHPL  227 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~-~~~M~~~g~~p-~~~t~~~li~~~~~~g~  227 (256)
                      +|...|++..+.  .| +...|..+-..|.+.|+.++|.+. +++..+.  .| +...|...-..+...|+
T Consensus        83 ~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           83 KAVECYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCc
Confidence            999999998873  36 467888999999999999877665 5766654  34 45566666666656554

>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=98.23  E-value=6.1e-05  Score=63.43  Aligned_cols=150  Identities=5%  Similarity=-0.014  Sum_probs=119.1

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCC-HHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEE-TILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~-~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      .+..+-..+.+.|+.++|+..+ +....  +.|+..    .+-..+...|+ +++|+..|++..+..  .-+...|+.+-
T Consensus        99 a~~~lg~~~~~~g~~~~Al~~~-~~al~--l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g  173 (382)
T 2h6f_A           99 VYDYFRAVLQRDERSERAFKLT-RDAIE--LNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHH-HHHHH--HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHH-HHHHH--hCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            4445556778899999998655 44433  234433    35666778896 999999999999886  66889999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC-CCC
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP-HPL  227 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~-~g~  227 (256)
                      ..|...|++++|...|++..+.  .| +...|..+-..+.+.|++++|++.|+++.+... -+...|+.+-..|.+ .|.
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~~  250 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGY  250 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHccCHHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCc
Confidence            9999999999999999999884  34 678899999999999999999999999987632 256788888888888 666


Q ss_pred             hHHHH
Q 025225          228 LRSKV  232 (256)
Q Consensus       228 ~~~a~  232 (256)
                      .++|+
T Consensus       251 ~~eA~  255 (382)
T 2h6f_A          251 NDRAV  255 (382)
T ss_dssp             CSHHH
T ss_pred             chHHH
Confidence            56663

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.21  E-value=4.3e-05  Score=52.67  Aligned_cols=113  Identities=17%  Similarity=0.075  Sum_probs=83.5

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+-..+...|++++|...|++..+..  ..+...|..+...|...|++++|.+.+++..+.. ..+...|..+-..|.+.
T Consensus        17 ~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   93 (131)
T 2vyi_A           17 TEGNEQMKVENFEAAVHFYGKAIELN--PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSSL   93 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHh
Confidence            35566777888888888888887774  5577888888888888899999988888877642 22467778888888888


Q ss_pred             CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCC
Q 025225          191 GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPL  227 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~  227 (256)
                      |++++|...|++..+.. ..+...+..+...+.+.|+
T Consensus        94 ~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           94 NKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhc
Confidence            89999988888877652 1244556666666655544

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.20  E-value=4.1e-05  Score=58.51  Aligned_cols=159  Identities=8%  Similarity=0.031  Sum_probs=108.1

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----H----------------HHHHHHHcCCHHHHHHHHHHHHhcCCCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----A----------------VLIELERQEETILAVKIFDIIRKQDWYQ  139 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~----------------li~~~~~~~~~~~a~~~~~~m~~~~~~~  139 (256)
                      -..+.+.|+.++|+..+. .....  .|+..    .                +-.++.+.|++++|...|++..+..  +
T Consensus        11 g~~~~~~g~~~~A~~~~~-~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p   85 (208)
T 3urz_A           11 VSAAIEAGQNGQAVSYFR-QTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA--P   85 (208)
T ss_dssp             HHHHHHTTCHHHHHHHHH-HHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T
T ss_pred             HHHHHHCCCHHHHHHHHH-HHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC--C
Confidence            455678999999986554 43322  23322    2                5567788999999999999999886  5


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCC--hhHHHHHHHHHHhCCCCCChhH--
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGS--PADAMNIYEDMIKSPDPPEELP--  214 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~--~~~a~~~~~~M~~~g~~p~~~t--  214 (256)
                      -+...|..+-..|...|++++|.+.|++..+.  .| +...|..+-..|...|+  .+.+...+....    .|+...  
T Consensus        86 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~a  159 (208)
T 3urz_A           86 NNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS----SPTKMQYA  159 (208)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh----CCCchhHH
Confidence            68899999999999999999999999999874  35 46778777777766553  344555555543    344333  


Q ss_pred             HHHHHHHhcCCCChHHHHHh--hhhhcCCCcccccch
Q 025225          215 FRILLKGLLPHPLLRSKVKK--DFEELFPEKHAYDPP  249 (256)
Q Consensus       215 ~~~li~~~~~~g~~~~a~~~--~~~~~~p~~~~~~~l  249 (256)
                      +...-.++...|++++|+..  ..-.+.|+......+
T Consensus       160 ~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l  196 (208)
T 3urz_A          160 RYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            33333445557889999883  334556765444433

>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=98.19  E-value=8.8e-05  Score=57.10  Aligned_cols=123  Identities=9%  Similarity=-0.004  Sum_probs=101.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      .=..+...|++++|.+.|++..+.. ..++...+..+-.+|...|++++|.+.|++..+.  .| +...|..+-..|.+.
T Consensus        13 ~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~   89 (228)
T 4i17_A           13 EGNDALNAKNYAVAFEKYSEYLKLT-NNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKSAAYRDM   89 (228)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHT-TTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHccCHHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHc
Confidence            4556778999999999999999886 2378888888999999999999999999998874  35 457888999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCCC-h-------hHHHHHHHHhcCCCChHHHHHhhhhhc
Q 025225          191 GSPADAMNIYEDMIKSPDPPE-E-------LPFRILLKGLLPHPLLRSKVKKDFEEL  239 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~g~~p~-~-------~t~~~li~~~~~~g~~~~a~~~~~~~~  239 (256)
                      |++++|.+.|++..+..  |+ .       ..|..+-..+...|++++|++...+-+
T Consensus        90 ~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al  144 (228)
T 4i17_A           90 KNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHAT  144 (228)
T ss_dssp             TCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHH
Confidence            99999999999988752  33 3       457777788889999999999444333

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.19  E-value=0.00015  Score=58.95  Aligned_cols=144  Identities=14%  Similarity=0.114  Sum_probs=87.8

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccC---CCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCC-----CHHHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLL---KMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQP-----DAYIYKDL  148 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-----~~~~y~~l  148 (256)
                      .+-..+...|+.++|+..+ ......+-   .+... .++..+.+.|+++.|.+.+++|.+.   .|     +..+...+
T Consensus       105 ~la~i~~~~g~~eeAL~~l-~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~---~~d~~~~~d~~l~~L  180 (310)
T 3mv2_B          105 LLATAQAILGDLDKSLETC-VEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA---IEDTVSGDNEMILNL  180 (310)
T ss_dssp             HHHHHHHHHTCHHHHHHHH-HHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---SCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHH-HHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CccccccchHHHHHH
Confidence            4456667778888887433 34333331   11222 3677888888888888888888765   35     35555666


Q ss_pred             HHHHHh--cC--CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----CC----CCChhHH
Q 025225          149 IIALAR--TG--KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----PD----PPEELPF  215 (256)
Q Consensus       149 i~~~~~--~g--~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----g~----~p~~~t~  215 (256)
                      ..+++.  .|  +..+|..+|+++.+.  .|+..+-..++.++.+.|++++|.+.++.+.+.     +.    .-|..+.
T Consensus       181 aea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~L  258 (310)
T 3mv2_B          181 AESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFL  258 (310)
T ss_dssp             HHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHH
T ss_pred             HHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHH
Confidence            656333  23  788888888887664  244334444555777888888888888866542     11    2355555


Q ss_pred             HHHHHHhcCCCC
Q 025225          216 RILLKGLLPHPL  227 (256)
Q Consensus       216 ~~li~~~~~~g~  227 (256)
                      -.+|......|+
T Consensus       259 aN~i~l~~~lgk  270 (310)
T 3mv2_B          259 ANQITLALMQGL  270 (310)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHHhCh
Confidence            344444444454

>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=98.19  E-value=0.00034  Score=52.91  Aligned_cols=116  Identities=9%  Similarity=-0.028  Sum_probs=97.3

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +-..+...|++++|...|++..     .|+...|..+-..|...|++++|.+.|++..+.. ..+...|..+-..|.+.|
T Consensus        12 ~g~~~~~~~~~~~A~~~~~~a~-----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~   85 (213)
T 1hh8_A           12 EGVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTE   85 (213)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhCCHHHHHHHHHHHc-----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcc
Confidence            4556778999999999998763     5688999999999999999999999999988743 236788999999999999


Q ss_pred             ChhHHHHHHHHHHhCCC--------------CC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPD--------------PP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~--------------~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++++|.+.|++..+..-              .| +...+..+-..|.+.|++++|.+
T Consensus        86 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  142 (213)
T 1hh8_A           86 KYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEE  142 (213)
T ss_dssp             CHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHH
Confidence            99999999999887521              11 22677888899999999999988

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.17  E-value=6.4e-05  Score=50.31  Aligned_cols=91  Identities=9%  Similarity=0.002  Sum_probs=69.8

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC---CHhhHHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP---DSQTYTEVIRGFL  188 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p---~~~t~~~li~~~~  188 (256)
                      +-..+...|++++|...|++..+..  ..+...|..+-..|...|++++|.+.|++..+..  |   +...|..+-..|.
T Consensus        12 ~~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~l~~~~~   87 (112)
T 2kck_A           12 EGVLQYDAGNYTESIDLFEKAIQLD--PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI--EDEYNKDVWAAKADALR   87 (112)
T ss_dssp             HHHHHHSSCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--CCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--cccchHHHHHHHHHHHH
Confidence            5556667788888888888877775  5567778888888888888888888888877642  3   4677777778888


Q ss_pred             Hc-CChhHHHHHHHHHHhC
Q 025225          189 KD-GSPADAMNIYEDMIKS  206 (256)
Q Consensus       189 ~~-g~~~~a~~~~~~M~~~  206 (256)
                      +. |++++|.+.|.+..+.
T Consensus        88 ~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           88 YIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             TCSSCSHHHHHHHHHHGGG
T ss_pred             HHhCCHHHHHHHHHHHhhc
Confidence            88 8888888888887765

>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=98.17  E-value=3.2e-05  Score=56.05  Aligned_cols=118  Identities=13%  Similarity=0.063  Sum_probs=75.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +-..+...|++++|...|++..+..  ..+..+|..+-..|...|++++|.+.|++..+.. ..+...|..+-..|.+.|
T Consensus        19 ~a~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~   95 (166)
T 1a17_A           19 QANDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALG   95 (166)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhc
Confidence            4455566777777777777776664  4567777777777777777777777777766532 124566777777777777


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHH--HHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFR--ILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~--~li~~~~~~g~~~~a~~  233 (256)
                      ++++|.+.|++..+... .+...+.  .....+.+.|++++|++
T Consensus        96 ~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~  138 (166)
T 1a17_A           96 KFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIA  138 (166)
T ss_dssp             CHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777777665421 1223332  23333556677777766

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.15  E-value=2.5e-05  Score=74.73  Aligned_cols=109  Identities=8%  Similarity=0.080  Sum_probs=58.2

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ..++..+.+.|+.++++ .++.+..+..-.|.+. .+..+|++.+++++....    . .   .|+...|..+=..|-..
T Consensus      1138 ~eVa~~~~~lGkyEEAI-eyL~mArk~~~e~~Idt~LafaYAKl~rleele~f----I-~---~~n~ad~~~iGd~le~e 1208 (1630)
T 1xi4_A         1138 MEVVQAANTSGNWEELV-KYLQMARKKARESYVETELIFALAKTNRLAELEEF----I-N---GPNNAHIQQVGDRCYDE 1208 (1630)
T ss_pred             HHHHHHHHHcCCHHHHH-HHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHH----H-h---CCCHHHHHHHHHHHHhc
Confidence            33455556666666665 3333333222111111 255555555555532222    1 1   23445555555566666


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          156 GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      |++++|..+|...         ..|..+...|++.|++++|.+.+++-
T Consensus      1209 g~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA 1247 (1630)
T 1xi4_A         1209 KMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA 1247 (1630)
T ss_pred             CCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh
Confidence            6666666666663         36777777777777777777776554

>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=98.15  E-value=2.3e-05  Score=58.12  Aligned_cols=149  Identities=12%  Similarity=0.010  Sum_probs=105.8

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH-
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA-  151 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~-  151 (256)
                      ...-..+.+.|+.++|+..+ +...+  ..|+..    .+-..+...|++++|...|+...+..   |+...+..+... 
T Consensus        10 ~~~a~~~~~~g~~~~A~~~~-~~al~--~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~---p~~~~~~~~~~~~   83 (176)
T 2r5s_A           10 LKQVSELLQQGEHAQALNVI-QTLSD--ELQSRGDVKLAKADCLLETKQFELAQELLATIPLEY---QDNSYKSLIAKLE   83 (176)
T ss_dssp             HHHHHHHHHTTCHHHHHHHH-HTSCH--HHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG---CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHH-HHHHH--HCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc---CChHHHHHHHHHH
Confidence            34456678899999998544 33322  223322    46777889999999999999987765   355444332211 


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCChH
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPLLR  229 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~~  229 (256)
                      +...+...+|...|++..+.  .| +...+..+-..|.+.|++++|...|++..+....+ +...+..+...|...|+.+
T Consensus        84 ~~~~~~~~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  161 (176)
T 2r5s_A           84 LHQQAAESPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGN  161 (176)
T ss_dssp             HHHHHTSCHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSC
T ss_pred             HHhhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCC
Confidence            22222334578888887763  35 47888899999999999999999999998875433 3568889999999999998


Q ss_pred             HHHH
Q 025225          230 SKVK  233 (256)
Q Consensus       230 ~a~~  233 (256)
                      +|+.
T Consensus       162 ~A~~  165 (176)
T 2r5s_A          162 AIAS  165 (176)
T ss_dssp             HHHH
T ss_pred             cHHH
Confidence            8877

>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=98.13  E-value=0.00014  Score=52.52  Aligned_cols=126  Identities=16%  Similarity=0.027  Sum_probs=93.3

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+..+-..+...|+.++|+..+.+......-.+... .+-..+...|++++|...|++..+..  ..+..+|..+-..|.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--KKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHH
Confidence            344455677889999999865544333222222222 46677888999999999999998885  567889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCC-CHhhHH--HHHHHHHHcCChhHHHHHHHHHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFP-DSQTYT--EVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p-~~~t~~--~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      ..|++++|.+.|++..+..  | +...+.  .+...+.+.|++++|.+.+.+..
T Consensus        93 ~~~~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVK--PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            9999999999999988742  3 344443  34444778899999999988754

>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=98.12  E-value=0.00012  Score=50.48  Aligned_cols=106  Identities=12%  Similarity=0.175  Sum_probs=82.7

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCC----HhhHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKED--LFPD----SQTYTEVI  184 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~----~~t~~~li  184 (256)
                      .+-..+...|++++|...|++..+..  ..+...|..+-..|...|++++|...|++..+..  ..++    ...|..+-
T Consensus         9 ~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la   86 (131)
T 1elr_A            9 ELGNDAYKKKDFDTALKHYDKAKELD--PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHH
Confidence            35566778899999999999988775  5678888899999999999999999999887642  1222    67788888


Q ss_pred             HHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          185 RGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       185 ~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      ..|.+.|++++|.+.|++..+.  .|+......+-.
T Consensus        87 ~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~  120 (131)
T 1elr_A           87 NSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQ  120 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHH
Confidence            8899999999999999988875  355555544443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.12  E-value=0.00014  Score=57.20  Aligned_cols=166  Identities=13%  Similarity=0.149  Sum_probs=116.0

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCC---cHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC-HHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKM---DIV-AVLIELERQEETILAVKIFDIIRKQDWYQPD-AYIYKDL  148 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~---~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~y~~l  148 (256)
                      .+...-..+.+.|+.++|+..+ +...... -.|   +.. .+-.++.+.|++++|...|+...+..+-.|. ...+..+
T Consensus        17 ~~~~~a~~~~~~g~~~~A~~~~-~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l   95 (261)
T 3qky_A           17 EAFERAMEFYNQGKYDRAIEYF-KAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYER   95 (261)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHH-HHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHH
Confidence            3344456778999999998555 5554432 221   111 3667788999999999999999987411223 4567777


Q ss_pred             HHHHHh--------cCCHHHHHHHHHHHHhCCCCCCH-hhH-----------------HHHHHHHHHcCChhHHHHHHHH
Q 025225          149 IIALAR--------TGKMNEAMQVWESMRKEDLFPDS-QTY-----------------TEVIRGFLKDGSPADAMNIYED  202 (256)
Q Consensus       149 i~~~~~--------~g~~~~a~~~~~~m~~~g~~p~~-~t~-----------------~~li~~~~~~g~~~~a~~~~~~  202 (256)
                      -.+|..        .|++++|...|++..+.  .|+. ..+                 -.+-..|.+.|++++|...|++
T Consensus        96 g~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  173 (261)
T 3qky_A           96 AMCYYKLSPPYELDQTDTRKAIEAFQLFIDR--YPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEA  173 (261)
T ss_dssp             HHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHH--CcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            778888        99999999999998874  2442 333                 3456778899999999999999


Q ss_pred             HHhCCCC-C-ChhHHHHHHHHhcCC----------CChHHHHHh--hhhhcCCCc
Q 025225          203 MIKSPDP-P-EELPFRILLKGLLPH----------PLLRSKVKK--DFEELFPEK  243 (256)
Q Consensus       203 M~~~g~~-p-~~~t~~~li~~~~~~----------g~~~~a~~~--~~~~~~p~~  243 (256)
                      ..+.... | ....+..+..+|...          |++++|+..  ......|+.
T Consensus       174 ~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~  228 (261)
T 3qky_A          174 VFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDS  228 (261)
T ss_dssp             HHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCC
Confidence            9875321 1 234667777777765          888888882  334445664

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.09  E-value=0.00028  Score=56.84  Aligned_cols=161  Identities=10%  Similarity=-0.004  Sum_probs=108.5

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhh---ccCCCcHH----HHHHHHHHc-CCHHHHHHHHHHHHhcCCCCCC----H
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVL---RLLKMDIV----AVLIELERQ-EETILAVKIFDIIRKQDWYQPD----A  142 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~----~li~~~~~~-~~~~~a~~~~~~m~~~~~~~p~----~  142 (256)
                      .+..+-..|.+.|+.++|+..+.+....   .|-.+...    .+-..|... |++++|+..|++..+...-..+    .
T Consensus        79 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~  158 (292)
T 1qqe_A           79 TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSN  158 (292)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHH
Confidence            4445567788999999998544333221   12111111    356667775 9999999999987754200111    4


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHh------hHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-----
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQ------TYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-----  211 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-----  211 (256)
                      .+|+.+-..|.+.|++++|.+.|++..+........      .|..+...|...|++++|...|++..+.  .|+     
T Consensus       159 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~  236 (292)
T 1qqe_A          159 KCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSR  236 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC----------
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcH
Confidence            578899999999999999999999998853222221      5677888899999999999999998764  222     


Q ss_pred             -hhHHHHHHHHhc--CCCChHHHHHhhhh
Q 025225          212 -ELPFRILLKGLL--PHPLLRSKVKKDFE  237 (256)
Q Consensus       212 -~~t~~~li~~~~--~~g~~~~a~~~~~~  237 (256)
                       ...+..++..|.  ..+++++|++....
T Consensus       237 ~~~~l~~l~~~~~~~~~~~~~~A~~~~~~  265 (292)
T 1qqe_A          237 ESNFLKSLIDAVNEGDSEQLSEHCKEFDN  265 (292)
T ss_dssp             -HHHHHHHHHHHHTTCTTTHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHhcc
Confidence             123445666664  55678888884433

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.08  E-value=0.00022  Score=57.31  Aligned_cols=155  Identities=10%  Similarity=0.050  Sum_probs=111.2

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCC--CCCC--HHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDW--YQPD--AYIY  145 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~--~~p~--~~~y  145 (256)
                      ...+..+...|+.++|++.+.+........++..       .+-..+...|++++|...|++..+...  ..+.  ..+|
T Consensus        79 ~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  158 (293)
T 2qfc_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIE  158 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHH
Confidence            3456778899999999865544333322222221       134445677899999999998875420  1122  5589


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCC-----HhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCC-ChhH
Q 025225          146 KDLIIALARTGKMNEAMQVWESMRKE-DLFPD-----SQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPP-EELP  214 (256)
Q Consensus       146 ~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~-----~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p-~~~t  214 (256)
                      +.+-..|...|++++|...|++..+. ...|+     ..+|+.+-..|.+.|++++|.+.+++..+.    +..+ -..+
T Consensus       159 ~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~  238 (293)
T 2qfc_A          159 NAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            99999999999999999999988731 11122     258889999999999999999999987643    2222 2567


Q ss_pred             HHHHHHHhcCCCChHHH
Q 025225          215 FRILLKGLLPHPLLRSK  231 (256)
Q Consensus       215 ~~~li~~~~~~g~~~~a  231 (256)
                      |..+-..|.+.|+.++|
T Consensus       239 ~~~lg~~y~~~g~~~~A  255 (293)
T 2qfc_A          239 YYQRGECLRKLEYEEAE  255 (293)
T ss_dssp             HHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHcCCcHHH
Confidence            88889999999999999

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.07  E-value=0.00031  Score=47.70  Aligned_cols=108  Identities=12%  Similarity=0.085  Sum_probs=79.3

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+..+...+...|+.++|...+ +...... -.+... .+...+.+.|++++|...|+++.+..  ..+..++..+...|
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~   87 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYY-QKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHH-HHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHH
Confidence            3445567788999999998555 4444332 112222 47788889999999999999999885  66889999999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGF  187 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~  187 (256)
                      ...|++++|.+.|++..+..  |+ ...+..+-..+
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~  121 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELD--PNNAEAKQNLGNAK  121 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHH
Confidence            99999999999999988742  43 34444443333

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.07  E-value=7.8e-05  Score=54.17  Aligned_cols=91  Identities=12%  Similarity=0.029  Sum_probs=80.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      +=..+.+.|++++|...|+...+..  +-+...|..+-.+|...|++++|.+.|++..+.  .| +...|..+-.+|.+.
T Consensus        42 lg~~~~~~g~~~eA~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l--~P~~~~~~~~lg~~~~~l  117 (151)
T 3gyz_A           42 YAYDFYNKGRIEEAEVFFRFLCIYD--FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL--GKNDYTPVFHTGQCQLRL  117 (151)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SSSCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CCCCcHHHHHHHHHHHHc
Confidence            5566778999999999999999886  668899999999999999999999999998874  35 467888899999999


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|...|++..+.
T Consensus       118 g~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          118 KAPLKAKECFELVIQH  133 (151)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            9999999999998876

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.06  E-value=0.00024  Score=57.15  Aligned_cols=154  Identities=11%  Similarity=0.023  Sum_probs=112.1

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhh-ccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC----HHHHH
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVL-RLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDWYQPD----AYIYK  146 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~  146 (256)
                      .+..+.+.++.++|...+ +.... ....|+..       .+-..+...+++++|...|++..+...-.++    ..+|+
T Consensus        81 ~i~~~~~~~~y~~a~~~~-~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~  159 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKV-WNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN  159 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHH-HHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHH-HHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            467788999999998554 44433 33333322       2444455667999999999998874312233    34799


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh----C-CCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHHh----CCCCCC-hhHH
Q 025225          147 DLIIALARTGKMNEAMQVWESMRK----E-DLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMIK----SPDPPE-ELPF  215 (256)
Q Consensus       147 ~li~~~~~~g~~~~a~~~~~~m~~----~-g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~----~g~~p~-~~t~  215 (256)
                      .+-..|...|++++|...|++..+    . +..|.. .+|..+-..|.+.|++++|.+.+++..+    .+-.+. ...|
T Consensus       160 ~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~  239 (293)
T 3u3w_A          160 AIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLY  239 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            999999999999999999999884    1 222222 4788999999999999999999997764    233333 5778


Q ss_pred             HHHHHHhcCCC-ChHHHHH
Q 025225          216 RILLKGLLPHP-LLRSKVK  233 (256)
Q Consensus       216 ~~li~~~~~~g-~~~~a~~  233 (256)
                      ..+-..|.+.| .+++|.+
T Consensus       240 ~~lg~~~~~~g~~~~~A~~  258 (293)
T 3u3w_A          240 YQRGECLRKLEYEEAEIED  258 (293)
T ss_dssp             HHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHH
Confidence            88888999999 4688887

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.06  E-value=7.5e-05  Score=51.76  Aligned_cols=92  Identities=15%  Similarity=0.112  Sum_probs=56.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +-..+...|++++|...|++..+..  ..+...|..+-..|...|++++|.+.|++..+.. ..+...|..+-..|.+.|
T Consensus        22 ~~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~   98 (133)
T 2lni_A           22 KGNECFQKGDYPQAMKHYTEAIKRN--PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMK   98 (133)
T ss_dssp             HHHHHHHTTCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHh
Confidence            4445556666666666666666553  3456666666666666667777776666665531 124556666666666667


Q ss_pred             ChhHHHHHHHHHHhC
Q 025225          192 SPADAMNIYEDMIKS  206 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~  206 (256)
                      ++++|.+.|++..+.
T Consensus        99 ~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           99 DYTKAMDVYQKALDL  113 (133)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHh
Confidence            777777666665543

>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=98.05  E-value=0.00018  Score=63.49  Aligned_cols=143  Identities=11%  Similarity=-0.043  Sum_probs=102.7

Q ss_pred             cccccccccCCCCCCccccccccchhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcH---H-HHHHHHHHcCCHHHH
Q 025225           50 ILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDI---V-AVLIELERQEETILA  125 (256)
Q Consensus        50 ~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~-~li~~~~~~~~~~~a  125 (256)
                      +..|++.....+..         ...+..+-..+.+.|+.++|...+ +...+.  .|+.   . .+-..+...|++++|
T Consensus         9 ~~~~~~al~~~p~~---------~~~~~~lg~~~~~~g~~~~A~~~~-~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A   76 (568)
T 2vsy_A            9 LLQLRAAVRHRPQD---------FVAWLMLADAELGMGDTTAGEMAV-QRGLAL--HPGHPEAVARLGRVRWTQQRHAEA   76 (568)
T ss_dssp             ------------CC---------HHHHHHHHHHHHHHTCHHHHHHHH-HHHHTT--STTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHhCCCC---------HHHHHHHHHHHHHcCCHHHHHHHH-HHHHHh--CCCCHHHHHHHHHHHHHCCCHHHH
Confidence            66666554433221         234445566778899999998555 444332  2332   2 467778899999999


Q ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc---CChhHHHHHHHH
Q 025225          126 VKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD---GSPADAMNIYED  202 (256)
Q Consensus       126 ~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~---g~~~~a~~~~~~  202 (256)
                      .+.|++..+..  .-+...|..+-..|.+.|++++|.+.|++..+.. ..+...+..+...|...   |+.++|.+.+++
T Consensus        77 ~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~  153 (568)
T 2vsy_A           77 AVLLQQASDAA--PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRA  153 (568)
T ss_dssp             HHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             HHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence            99999999886  5678899999999999999999999999988742 12567888999999999   999999999999


Q ss_pred             HHhCC
Q 025225          203 MIKSP  207 (256)
Q Consensus       203 M~~~g  207 (256)
                      ..+.+
T Consensus       154 al~~~  158 (568)
T 2vsy_A          154 AVAQG  158 (568)
T ss_dssp             HHHHT
T ss_pred             HHhcC
Confidence            88653

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.05  E-value=8.2e-05  Score=60.51  Aligned_cols=119  Identities=9%  Similarity=0.043  Sum_probs=95.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-----CHhhHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-----DSQTYTEVIR  185 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-----~~~t~~~li~  185 (256)
                      .+-.++...|++++|++++.+....+.-.-+...+-.++..|.+.|+.+.|.+.+++|.+.  .|     +..+...|..
T Consensus       105 ~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~~l~~Lae  182 (310)
T 3mv2_B          105 LLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDNEMILNLAE  182 (310)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CccccccchHHHHHHHH
Confidence            4667788899999999999998766511247788889999999999999999999999874  46     3667777777


Q ss_pred             HHHH--cC--ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          186 GFLK--DG--SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       186 ~~~~--~g--~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++..  .|  +.++|..+|+++.+.  .|+..+-..++.++.+.|++++|-+
T Consensus       183 a~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~  232 (310)
T 3mv2_B          183 SYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQG  232 (310)
T ss_dssp             HHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHH
Confidence            7443  34  899999999999776  3554555666668999999999988

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.04  E-value=0.0008  Score=51.80  Aligned_cols=151  Identities=12%  Similarity=0.118  Sum_probs=105.9

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhc-cCCCc---HH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH-HHHHHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLR-LLKMD---IV-AVLIELERQEETILAVKIFDIIRKQDWYQPDA-YIYKDLIIA  151 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~-~~~~~---~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~y~~li~~  151 (256)
                      ..-..+.+.|+.++|+..| +..... .-.|.   .. .+-.++.+.|++++|...|++..+..+-.+.. ..+-.+-.+
T Consensus         9 ~~a~~~~~~g~~~~A~~~~-~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~   87 (225)
T 2yhc_A            9 ATAQQKLQDGNWRQAITQL-EALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLT   87 (225)
T ss_dssp             HHHHHHHHHTCHHHHHHHH-HHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHH-HHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHH
Confidence            3455678899999998655 444432 22232   12 47788899999999999999998875222322 133333333


Q ss_pred             HHh------------------cCCHHHHHHHHHHHHhCCCCCCHh-hH-----------------HHHHHHHHHcCChhH
Q 025225          152 LAR------------------TGKMNEAMQVWESMRKEDLFPDSQ-TY-----------------TEVIRGFLKDGSPAD  195 (256)
Q Consensus       152 ~~~------------------~g~~~~a~~~~~~m~~~g~~p~~~-t~-----------------~~li~~~~~~g~~~~  195 (256)
                      +..                  .|+.++|...|++..+.  .|+.. .+                 -.+-..|.+.|++++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~  165 (225)
T 2yhc_A           88 NMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVA  165 (225)
T ss_dssp             HHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHH
Confidence            333                  57899999999999874  35432 22                 234456788999999


Q ss_pred             HHHHHHHHHhCCCCCC----hhHHHHHHHHhcCCCChHHHHH
Q 025225          196 AMNIYEDMIKSPDPPE----ELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       196 a~~~~~~M~~~g~~p~----~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |...|++..+.-  |+    ...+..+..+|.+.|+.++|.+
T Consensus       166 A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~  205 (225)
T 2yhc_A          166 VVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEK  205 (225)
T ss_dssp             HHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHH
Confidence            999999998762  33    2568889999999999999988

>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=98.04  E-value=8.1e-05  Score=52.16  Aligned_cols=102  Identities=13%  Similarity=0.085  Sum_probs=79.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCC----HhhHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKED--LFPD----SQTYTEVIR  185 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~----~~t~~~li~  185 (256)
                      +=+.+.+.|++++|++.|++..+..  +-+...|+.+-.+|.+.|++++|.+.|++..+..  ..++    ..+|..+=.
T Consensus        14 lG~~~~~~~~~~~A~~~y~~Al~~~--p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~   91 (127)
T 4gcn_A           14 LGNAAYKQKDFEKAHVHYDKAIELD--PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGN   91 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHH
Confidence            5567888999999999999988885  5678899999999999999999999999887531  1122    135666777


Q ss_pred             HHHHcCChhHHHHHHHHHHhCCCCCChhHHHH
Q 025225          186 GFLKDGSPADAMNIYEDMIKSPDPPEELPFRI  217 (256)
Q Consensus       186 ~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~  217 (256)
                      .|...|++++|.+.|++-.+.  .||..+...
T Consensus        92 ~~~~~~~~~~A~~~~~kal~~--~~~~~~~~~  121 (127)
T 4gcn_A           92 AFQKQNDLSLAVQWFHRSLSE--FRDPELVKK  121 (127)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--SCCHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhh--CcCHHHHHH
Confidence            788899999999999987664  456554443

>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=98.02  E-value=8.8e-05  Score=54.72  Aligned_cols=119  Identities=8%  Similarity=0.054  Sum_probs=86.5

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH-HHhcCCH--H
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA-LARTGKM--N  159 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~-~~~~g~~--~  159 (256)
                      ...|+.++|+..+.+......-.++.. .+-..+...|++++|...|++..+..  ..+...|..+-.. |...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR--GENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--CSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhcCCcchH
Confidence            455666666644433332222222222 46677888999999999999998875  5577888888888 7789998  9


Q ss_pred             HHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          160 EAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      +|...|++..+..  | +...|..+-..|.+.|++++|...|++..+.
T Consensus        99 ~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           99 QTRAMIDKALALD--SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            9999999988742  4 4677888888999999999999999998876

>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=98.00  E-value=5.2e-05  Score=55.98  Aligned_cols=125  Identities=6%  Similarity=0.060  Sum_probs=95.4

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH-HHHcCCh-
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRG-FLKDGSP-  193 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~-~~~~g~~-  193 (256)
                      +...|++++|...++...+..  ..+...|..+-..|...|++++|...|++..+.. ..+...|..+-.. |.+.|++ 
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~   96 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHM   96 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCC
T ss_pred             hhhccCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcc
Confidence            345688899999999988775  5688999999999999999999999999988742 1256677777777 7789998 


Q ss_pred             -hHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHh--hhhhcCCCcc
Q 025225          194 -ADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKK--DFEELFPEKH  244 (256)
Q Consensus       194 -~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~--~~~~~~p~~~  244 (256)
                       ++|...|++..+.. .-+...+..+...|...|++++|...  ......|+..
T Consensus        97 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~  149 (177)
T 2e2e_A           97 TAQTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPRI  149 (177)
T ss_dssp             CHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTS
T ss_pred             hHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCc
Confidence             99999999988763 22467788888999999999999983  3334455543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.00  E-value=0.00015  Score=51.56  Aligned_cols=92  Identities=16%  Similarity=0.046  Sum_probs=75.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +-..+.+.|++++|...|+...+..  +.+...|..+-.+|...|++++|...|++..+.. +.+...|..+-..|...|
T Consensus        24 ~a~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g  100 (142)
T 2xcb_A           24 LGFNQYQAGKWDDAQKIFQALCMLD--HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLG  100 (142)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHccHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcC
Confidence            4556778899999999999988876  5678888888889999999999999999888742 124567778888888999


Q ss_pred             ChhHHHHHHHHHHhC
Q 025225          192 SPADAMNIYEDMIKS  206 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~  206 (256)
                      ++++|.+.|++..+.
T Consensus       101 ~~~~A~~~~~~al~~  115 (142)
T 2xcb_A          101 DLDGAESGFYSARAL  115 (142)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999887754

>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=97.99  E-value=0.00054  Score=45.99  Aligned_cols=93  Identities=14%  Similarity=0.033  Sum_probs=75.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+-..+...|++++|...|+...+..  +.+...|..+-..|...|++++|.+.+++..+.. +.+...|..+-..|.+.
T Consensus         9 ~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~   85 (118)
T 1elw_A            9 EKGNKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFL   85 (118)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHH
Confidence            35566778899999999999888775  5578888888888889999999999998887642 12567788888888899


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|.+.|++..+.
T Consensus        86 ~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           86 NRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             TCHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHc
Confidence            9999999999888765

>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=97.99  E-value=0.0002  Score=49.59  Aligned_cols=91  Identities=19%  Similarity=0.097  Sum_probs=75.3

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      +=..+.+.|++++|...|++..+..  ..+...|..+-.+|.+.|++++|.+.|++..+.  .| +...|..+-..|...
T Consensus        10 ~g~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~   85 (126)
T 3upv_A           10 EGKEYFTKSDWPNAVKAYTEMIKRA--PEDARGYSNRAAALAKLMSFPEAIADCNKAIEK--DPNFVRAYIRKATAQIAV   85 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHH
Confidence            3455678899999999999888875  567888999999999999999999999988774  24 467788888888899


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|.+.|++..+.
T Consensus        86 ~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           86 KEYASALETLDAARTK  101 (126)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             hCHHHHHHHHHHHHHh
Confidence            9999999999887764

>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=97.97  E-value=8.7e-05  Score=59.75  Aligned_cols=122  Identities=11%  Similarity=0.039  Sum_probs=93.8

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCC----HhhHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDA----YIYKDLIIALARTGKMNEAMQVWESMRKEDL-FPD----SQTYTE  182 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~----~~t~~~  182 (256)
                      .+..+...|++++|.+.+++..+.....|+.    ..|..+...+...|++++|.+.|++..+... .+|    ..+|+.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            4677889999999999999988754233442    2344566667777899999999999987422 233    236899


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHh----C-CCCCCh-hHHHHHHHHhcCCCChHHHHH
Q 025225          183 VIRGFLKDGSPADAMNIYEDMIK----S-PDPPEE-LPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       183 li~~~~~~g~~~~a~~~~~~M~~----~-g~~p~~-~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +-..|...|++++|.+.|++..+    . +..|.. .+|..+-..|.+.|++++|++
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~  217 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLY  217 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            99999999999999999999874    2 222333 378889999999999999998

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.97  E-value=0.00059  Score=46.70  Aligned_cols=116  Identities=13%  Similarity=-0.033  Sum_probs=86.4

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+..+...+...|+.++|+..+.+......-.+... .+-..+...|++++|.+.++...+..  ..+...|..+-..|.
T Consensus        14 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~   91 (131)
T 2vyi_A           14 RLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID--PAYSKAYGRMGLALS   91 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC--ccCHHHHHHHHHHHH
Confidence            344456677889999999865543333222122222 46777889999999999999998875  567889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCCh
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  193 (256)
                      ..|++++|.+.|++..+.. +.+...+..+...+.+.|+.
T Consensus        92 ~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           92 SLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             HhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence            9999999999999988742 12567777777787777764

>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=97.96  E-value=0.00018  Score=65.28  Aligned_cols=147  Identities=10%  Similarity=-0.011  Sum_probs=116.7

Q ss_pred             hcCCCcHHHHHHHHHHHh------hccCCCcH---H-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           84 KRFKDDEEKLQKFIKTHV------LRLLKMDI---V-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~------~~~~~~~~---~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      ...++.++|++.+ +...      .....|+.   . .+-.++...|++++|.+.|++..+..  .-+...|..+-.+|.
T Consensus       402 ~~~~~~~~A~~~~-~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~  478 (681)
T 2pzi_A          402 TVLSQPVQTLDSL-RAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV--GWRWRLVWYRAVAEL  478 (681)
T ss_dssp             TTTCCHHHHHHHH-HHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHH-HHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC--cchHHHHHHHHHHHH
Confidence            6789999998555 4443      11222332   2 36667889999999999999999886  568889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ..|++++|.+.|++..+.  .| +...|..+-..|.+.|++++ .+.|++..+.. .-+...|..+-..|.+.|++++|+
T Consensus       479 ~~g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~  554 (681)
T 2pzi_A          479 LTGDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAV  554 (681)
T ss_dssp             HHTCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHH
Confidence            999999999999998874  35 56788889999999999999 99999988653 125568889999999999999999


Q ss_pred             Hhhhh
Q 025225          233 KKDFE  237 (256)
Q Consensus       233 ~~~~~  237 (256)
                      +...+
T Consensus       555 ~~~~~  559 (681)
T 2pzi_A          555 RTLDE  559 (681)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            94443

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.96  E-value=0.0003  Score=58.69  Aligned_cols=153  Identities=7%  Similarity=-0.050  Sum_probs=112.0

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhc-cCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCC-----CHHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLR-LLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDWYQP-----DAYIYK  146 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-----~~~~y~  146 (256)
                      -..+...|+.++|+..+ +..... .-.++..       .+-..+...|++++|...+++..+...-.+     ...+++
T Consensus       110 g~~~~~~g~~~~A~~~~-~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          110 GMYELDQREYLSAIKFF-KKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHTTCHHHHHHHH-HHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHH-HHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            34567889999998555 444332 2223322       366677889999999999998765421112     246788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CC-CCChhHHH
Q 025225          147 DLIIALARTGKMNEAMQVWESMRKED-LFPD----SQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PD-PPEELPFR  216 (256)
Q Consensus       147 ~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~-~p~~~t~~  216 (256)
                      .+-..|...|++++|.+.|++..+.. -.++    ..+|+.+-..|...|++++|.+.|++..+.    +- .....++.
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  268 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYF  268 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHH
Confidence            88899999999999999999877521 0122    247888999999999999999999988762    33 33466788


Q ss_pred             HHHHHhcCCCChHHHHH
Q 025225          217 ILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       217 ~li~~~~~~g~~~~a~~  233 (256)
                      .+-..|.+.|++++|.+
T Consensus       269 ~l~~~~~~~g~~~~A~~  285 (383)
T 3ulq_A          269 LITQIHYKLGKIDKAHE  285 (383)
T ss_dssp             HHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHH
Confidence            89999999999999988

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=97.95  E-value=0.0014  Score=57.29  Aligned_cols=146  Identities=12%  Similarity=0.040  Sum_probs=105.5

Q ss_pred             CCCcH-------HHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHHH
Q 025225           86 FKDDE-------EKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPD-AYIYKDLIIALA  153 (256)
Q Consensus        86 ~~~~~-------~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~y~~li~~~~  153 (256)
                      .|+.+       +|.. +++...+ .+.|+..    .+...+.+.|++++|..+|+...+..  ..+ ...|......+.
T Consensus       292 ~g~~~~a~~~~~~A~~-~~~~Al~-~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~  367 (530)
T 2ooe_A          292 KGDMNNAKLFSDEAAN-IYERAIS-TLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE--DIDPTLVYIQYMKFAR  367 (530)
T ss_dssp             TTCCHHHHHHHHHHHH-HHHHHTT-TTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS--SSCHHHHHHHHHHHHH
T ss_pred             ccchhhhhhhhHHHHH-HHHHHHH-HhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcc--ccCchHHHHHHHHHHH
Confidence            68876       6663 4344432 1235433    47778888999999999999999864  234 358999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCC-HhhHH--HHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHH
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPD-SQTYT--EVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRS  230 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~-~~t~~--~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~  230 (256)
                      +.|++++|.++|++..+.  .|+ ...|-  .++. +...|+.++|..+|++..+.. +-+...|..++..+.+.|+.++
T Consensus       368 ~~~~~~~A~~~~~~Al~~--~~~~~~~~~~~a~~~-~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~  443 (530)
T 2ooe_A          368 RAEGIKSGRMIFKKARED--ARTRHHVYVTAALME-YYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNN  443 (530)
T ss_dssp             HHHHHHHHHHHHHHHHTC--TTCCTHHHHHHHHHH-HHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHH
T ss_pred             HhcCHHHHHHHHHHHHhc--cCCchHHHHHHHHHH-HHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhh
Confidence            999999999999998875  232 22222  2222 336899999999999887652 2257889999999999999999


Q ss_pred             HHHhhhhhc
Q 025225          231 KVKKDFEEL  239 (256)
Q Consensus       231 a~~~~~~~~  239 (256)
                      |.....+.+
T Consensus       444 Ar~~~~~al  452 (530)
T 2ooe_A          444 TRVLFERVL  452 (530)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988444333

>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=97.95  E-value=0.0002  Score=51.57  Aligned_cols=91  Identities=12%  Similarity=0.013  Sum_probs=77.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      +-..+.+.|++++|...|+...+..  ..+...|..+-.+|...|++++|.+.|++..+.  .| +...|..+-..|...
T Consensus        27 ~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~  102 (148)
T 2vgx_A           27 LAFNQYQSGXYEDAHXVFQALCVLD--HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM--DIXEPRFPFHAAECLLQX  102 (148)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCCchHHHHHHHHHHHc
Confidence            5566778899999999999988876  568888999989999999999999999998774  24 557788888889999


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|.+.|++..+.
T Consensus       103 g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A          103 GELAEAESGLFLAQEL  118 (148)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999999988764

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.94  E-value=0.00012  Score=58.95  Aligned_cols=53  Identities=13%  Similarity=0.085  Sum_probs=26.0

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      .+...|++++|...|++..+..  +-+...+..+-..|...|++++|...+++..
T Consensus       126 ~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~  178 (287)
T 3qou_A          126 QLMQESNYTDALPLLXDAWQLS--NQNGEIGLLLAETLIALNRSEDAEAVLXTIP  178 (287)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHT--TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSC
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC--CcchhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3444455555555555544443  3344445555555555555555555555443

>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=0.00049  Score=60.14  Aligned_cols=153  Identities=13%  Similarity=0.013  Sum_probs=112.1

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCc-H-H---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMD-I-V---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDL  148 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~-~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~l  148 (256)
                      ..|......+.+.|+.++|...+ +.....  .|+ . .   .+...+.+.|++++|.++|++..+..  ..+...|-..
T Consensus       322 ~l~~~~~~~~~~~g~~~~A~~~~-~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~--~~~~~~~~~~  396 (530)
T 2ooe_A          322 LLYFAYADYEESRMKYEKVHSIY-NRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA--RTRHHVYVTA  396 (530)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHH-HHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT--TCCTHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHH-HHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhcc--CCchHHHHHH
Confidence            34555566777889999997544 555442  332 1 1   46667778999999999999998775  2233333322


Q ss_pred             H-HHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC-CCCC--hhHHHHHHHHhc
Q 025225          149 I-IALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP-DPPE--ELPFRILLKGLL  223 (256)
Q Consensus       149 i-~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g-~~p~--~~t~~~li~~~~  223 (256)
                      . ..+...|+.++|..+|++..+.  .| +...|..++..+.+.|+.++|..+|++..+.+ ..|+  ...|...++-..
T Consensus       397 a~~~~~~~~~~~~A~~~~e~al~~--~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~  474 (530)
T 2ooe_A          397 ALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFES  474 (530)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCChhHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHH
Confidence            2 2234689999999999988764  25 57889999999999999999999999998763 3343  457888888888


Q ss_pred             CCCChHHHHH
Q 025225          224 PHPLLRSKVK  233 (256)
Q Consensus       224 ~~g~~~~a~~  233 (256)
                      +.|+.+++..
T Consensus       475 ~~G~~~~~~~  484 (530)
T 2ooe_A          475 NIGDLASILK  484 (530)
T ss_dssp             HSSCHHHHHH
T ss_pred             HcCCHHHHHH
Confidence            8999888776

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.92  E-value=0.00024  Score=51.75  Aligned_cols=92  Identities=13%  Similarity=0.055  Sum_probs=71.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  191 (256)
                      +-..+.+.|++++|++.|++..+..  .-+...|..+-.+|.+.|++++|...|++..+.. ..+...|..+-..|.+.|
T Consensus        17 ~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g   93 (164)
T 3sz7_A           17 EGNAAMARKEYSKAIDLYTQALSIA--PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLARFDMA   93 (164)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcc
Confidence            4556677888888888888887775  4577888888888888888888888888877642 124677788888888888


Q ss_pred             ChhHHHHHHHHHHhC
Q 025225          192 SPADAMNIYEDMIKS  206 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~  206 (256)
                      ++++|.+.|++..+.
T Consensus        94 ~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           94 DYKGAKEAYEKGIEA  108 (164)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh
Confidence            888888888887754

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.92  E-value=5.1e-06  Score=67.12  Aligned_cols=220  Identities=10%  Similarity=-0.057  Sum_probs=143.0

Q ss_pred             ccccCCchHHHHHHHHHhcCCC---------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS---------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEA   76 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~---------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~   76 (256)
                      +.+.|+.+.|.+.++...+...         +..+-..+...++...+     +..+++.........   ........+
T Consensus        15 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~~~~~---~~~~~~~~~   86 (338)
T 3ro2_A           15 LCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKA-----LEYHHHDLTLARTIG---DQLGEAKAS   86 (338)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHHHHHT---CHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHHhhccc---ccHHHHHHH
Confidence            4568899999999998654321         33444455556666666     776655432211000   000112234


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCc------HH-HHHHHHHHcCC--------------------HHHHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMD------IV-AVLIELERQEE--------------------TILAVKIF  129 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~-~li~~~~~~~~--------------------~~~a~~~~  129 (256)
                      ..+-..+...|+.++|...+.+......-.++      .. .+-..+...|+                    +++|.+.+
T Consensus        87 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~  166 (338)
T 3ro2_A           87 GNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLY  166 (338)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHH
Confidence            44566778899999998655433322111122      11 36667778888                    99999999


Q ss_pred             HHHHhc----CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HhhHHHHHHHHHHcCChhHHHHHH
Q 025225          130 DIIRKQ----DWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKED-LFPD----SQTYTEVIRGFLKDGSPADAMNIY  200 (256)
Q Consensus       130 ~~m~~~----~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~li~~~~~~g~~~~a~~~~  200 (256)
                      ++..+.    +.......++..+-..|...|++++|.+.+++..+.. -.++    ..++..+...|...|++++|.+.+
T Consensus       167 ~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  246 (338)
T 3ro2_A          167 EENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYY  246 (338)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            876533    2011224578888899999999999999999876521 0112    347888899999999999999999


Q ss_pred             HHHHhC----CCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          201 EDMIKS----PDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       201 ~~M~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++..+.    +-.+ ...++..+...|...|++++|.+
T Consensus       247 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  284 (338)
T 3ro2_A          247 KKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAID  284 (338)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            987643    1111 15677888899999999999988

>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=97.92  E-value=0.00031  Score=49.12  Aligned_cols=93  Identities=10%  Similarity=-0.065  Sum_probs=75.1

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+-..+...|++++|...|+...+..  ..+...|..+-..|...|++++|...|++..+.. +.+...|..+-..|.+.
T Consensus        14 ~~g~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~   90 (137)
T 3q49_B           14 EQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEM   90 (137)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHH
Confidence            35667778899999999999888775  5578888888888999999999999998887743 12567788888888899


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|...|.+..+.
T Consensus        91 ~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           91 ESYDEAIANLQRAYSL  106 (137)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHH
Confidence            9999999998887653

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.90  E-value=2.6e-05  Score=56.42  Aligned_cols=128  Identities=9%  Similarity=0.020  Sum_probs=97.7

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHH
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADA  196 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a  196 (256)
                      ..|++++|+..+.......  +-+...+-.+-..|.+.|++++|.+.|++..+.  .| +...|..+-..|.+.|++++|
T Consensus         9 ~~~~~e~ai~~~~~a~~~~--p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A   84 (150)
T 4ga2_A            9 SKADVERYIASVQGSTPSP--RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEENTDKA   84 (150)
T ss_dssp             CHHHHHHHHHHHHHHSCSH--HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HcChHHHHHHHHHHhcccC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCchHHH
Confidence            4578899999888876543  223445666788899999999999999998874  35 578899999999999999999


Q ss_pred             HHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCChHHHHHh---hhhhcCCCc-ccccchhH
Q 025225          197 MNIYEDMIKSPDPP-EELPFRILLKGLLPHPLLRSKVKK---DFEELFPEK-HAYDPPEE  251 (256)
Q Consensus       197 ~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~---~~~~~~p~~-~~~~~li~  251 (256)
                      ...|++..+.  .| +...|..+-..|.+.|+++++.+.   ....+.|+. ..|.....
T Consensus        85 ~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~  142 (150)
T 4ga2_A           85 VECYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQ  142 (150)
T ss_dssp             HHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHH
Confidence            9999998875  34 467788888999999998887662   334566753 34444333

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.87  E-value=8.1e-06  Score=68.11  Aligned_cols=220  Identities=10%  Similarity=-0.066  Sum_probs=142.8

Q ss_pred             ccccCCchHHHHHHHHHhcCCC---------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS---------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEA   76 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~---------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~   76 (256)
                      +.+.|+.+.|.+.|+...+...         |..+-..+...++...+     +..+++..........   .......+
T Consensus        19 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~~~~~~---~~~~~~~~   90 (406)
T 3sf4_A           19 LCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKA-----LEYHHHDLTLARTIGD---QLGEAKAS   90 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHHHHTTC---HHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHH-----HHHHHHHHHHHHhccc---cHHHHHHH
Confidence            4567899999999988654321         33444455566666666     7766554322111000   00112234


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCc------HH-HHHHHHHHcCC--------------------HHHHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMD------IV-AVLIELERQEE--------------------TILAVKIF  129 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~-~li~~~~~~~~--------------------~~~a~~~~  129 (256)
                      ..+-..+...|+.++|+..+.+......-.++      .. .+-..+...|+                    +++|.+.+
T Consensus        91 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~  170 (406)
T 3sf4_A           91 GNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFY  170 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHH
Confidence            44566778899999998544332222111112      11 36667778889                    99999998


Q ss_pred             HHHHhc----CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HhhHHHHHHHHHHcCChhHHHHHH
Q 025225          130 DIIRKQ----DWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKED-LFPD----SQTYTEVIRGFLKDGSPADAMNIY  200 (256)
Q Consensus       130 ~~m~~~----~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~li~~~~~~g~~~~a~~~~  200 (256)
                      ++..+.    +.......+|..+-..|...|++++|.+.|++..+.. -.++    ..+|..+-..|...|++++|...+
T Consensus       171 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  250 (406)
T 3sf4_A          171 EENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYY  250 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHH
Confidence            876543    2011224578888899999999999999999887521 1122    347888899999999999999999


Q ss_pred             HHHHhC----CCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          201 EDMIKS----PDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       201 ~~M~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++..+.    +-.+ ...++..+...|...|++++|.+
T Consensus       251 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  288 (406)
T 3sf4_A          251 KKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAID  288 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHH
Confidence            987643    2111 15678888999999999999988

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.86  E-value=0.0002  Score=49.68  Aligned_cols=92  Identities=12%  Similarity=0.097  Sum_probs=65.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLK  189 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~  189 (256)
                      .+-..+.+.|++++|...|++..+..  .-+...|..+-.++...|++++|...|++..+.  .| +...|..+-..|.+
T Consensus        22 ~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           22 EEGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            34455667778888888888777764  456777777777777888888888888777663  24 45667777777777


Q ss_pred             cCChhHHHHHHHHHHhC
Q 025225          190 DGSPADAMNIYEDMIKS  206 (256)
Q Consensus       190 ~g~~~~a~~~~~~M~~~  206 (256)
                      .|++++|...|++..+.
T Consensus        98 ~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           98 EHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            88888888888777654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.84  E-value=0.00068  Score=56.45  Aligned_cols=152  Identities=9%  Similarity=-0.074  Sum_probs=110.5

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhh-ccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCC-----CHHHHHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVL-RLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDWYQP-----DAYIYKD  147 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-----~~~~y~~  147 (256)
                      ..+...|+.++|+..+ +.... ..-.++..       .+-..+...|++++|...+++..+...-.+     ...+++.
T Consensus       109 ~~~~~~g~~~~A~~~~-~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  187 (378)
T 3q15_A          109 MYEFDQKEYVEAIGYY-REAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFV  187 (378)
T ss_dssp             HHHHHTTCHHHHHHHH-HHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHH
T ss_pred             HHHHHHCCHHHHHHHH-HHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHH
Confidence            3456889999998555 44433 22223322       366678889999999999998764320111     2567888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCChhHHHHH
Q 025225          148 LIIALARTGKMNEAMQVWESMRKE----DLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPEELPFRIL  218 (256)
Q Consensus       148 li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~~~t~~~l  218 (256)
                      +-..|...|++++|.+.|++..+.    +-.+ ...+++.+-..|...|++++|.+.|++..+.    +-.....++..+
T Consensus       188 lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  267 (378)
T 3q15_A          188 IAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGL  267 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHH
Confidence            899999999999999999987652    1111 2356788888899999999999999988761    222236778889


Q ss_pred             HHHhcCCCChHHHHH
Q 025225          219 LKGLLPHPLLRSKVK  233 (256)
Q Consensus       219 i~~~~~~g~~~~a~~  233 (256)
                      -..|.+.|++++|.+
T Consensus       268 a~~~~~~g~~~~A~~  282 (378)
T 3q15_A          268 SWTLCKAGQTQKAFQ  282 (378)
T ss_dssp             HHHHHHTTCHHHHHH
T ss_pred             HHHHHHCCCHHHHHH
Confidence            999999999999988

>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=97.83  E-value=7.1e-05  Score=54.00  Aligned_cols=115  Identities=13%  Similarity=0.007  Sum_probs=86.9

Q ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          127 KIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       127 ~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      ..|++..+..  ..+...+..+-..+...|++++|...|++....  .| +...|..+-..|.+.|++++|.+.|++..+
T Consensus         8 ~~~~~al~~~--p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   83 (148)
T 2vgx_A            8 GTIAMLNEIS--SDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVL--DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAV   83 (148)
T ss_dssp             CSHHHHTTCC--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHcCC--HhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHc--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            3445544443  335567777888899999999999999998774  24 677888888899999999999999999887


Q ss_pred             CCCCCChhHHHHHHHHhcCCCChHHHHHh--hhhhcCCCcccc
Q 025225          206 SPDPPEELPFRILLKGLLPHPLLRSKVKK--DFEELFPEKHAY  246 (256)
Q Consensus       206 ~g~~p~~~t~~~li~~~~~~g~~~~a~~~--~~~~~~p~~~~~  246 (256)
                      .. +-+...|..+-.+|...|++++|.+.  ..-.+.|+...+
T Consensus        84 l~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~  125 (148)
T 2vgx_A           84 MD-IXEPRFPFHAAECLLQXGELAEAESGLFLAQELIANXPEF  125 (148)
T ss_dssp             HS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCGGG
T ss_pred             cC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCCcc
Confidence            53 22567788899999999999999983  233444554433

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.82  E-value=0.0001  Score=55.32  Aligned_cols=147  Identities=15%  Similarity=-0.003  Sum_probs=98.8

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHHHhc
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~~y~~li~~~~~~  155 (256)
                      ...|+.++|.. ..+....  ..+...    .+-..+...|++++|...+++..+.    +.......+++.+-..|...
T Consensus         3 ~~~g~~~~A~~-~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~   79 (203)
T 3gw4_A            3 FEAHDYALAER-QAQALLA--HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMA   79 (203)
T ss_dssp             ----CHHHHHH-HHHHHHT--STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHT
T ss_pred             cccccHHHHHH-HHHHhcC--ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHc
Confidence            35678888864 2222222  111222    3666777899999999999987752    10123456788888899999


Q ss_pred             CCHHHHHHHHHHHHhC----CCCC--CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCC-CChhHHHHHHHHhcC
Q 025225          156 GKMNEAMQVWESMRKE----DLFP--DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDP-PEELPFRILLKGLLP  224 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~----g~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~-p~~~t~~~li~~~~~  224 (256)
                      |++++|.+.|++..+.    +-.|  ....+..+-..|...|++++|.+.+++..+.    +-. +-..++..+-..+..
T Consensus        80 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~  159 (203)
T 3gw4_A           80 GNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQ  159 (203)
T ss_dssp             TCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence            9999999999987653    2111  1355778888889999999999999887642    211 123346778888999


Q ss_pred             CCChHHHHH
Q 025225          225 HPLLRSKVK  233 (256)
Q Consensus       225 ~g~~~~a~~  233 (256)
                      .|++++|.+
T Consensus       160 ~g~~~~A~~  168 (203)
T 3gw4_A          160 EKNLLEAQQ  168 (203)
T ss_dssp             TTCHHHHHH
T ss_pred             CcCHHHHHH
Confidence            999999887

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.81  E-value=0.0012  Score=45.41  Aligned_cols=113  Identities=12%  Similarity=-0.027  Sum_probs=82.3

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      ..+..+-..+.+.|+.++|+..+ +...... -.+... .+-..+...|++++|.+.|++..+..  ..+...|..+-..
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~-~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~   93 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHY-TEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE--PTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHH-HHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHH-HHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCchHHHHHHHHH
Confidence            45556677888999999998555 4443322 112222 36667788999999999999999885  5678899999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcC
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDG  191 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g  191 (256)
                      |.+.|++++|.+.|++..+.  .|+ ...+..+-..+.+.|
T Consensus        94 ~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKALDL--DSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CGGGTHHHHHHHHHHHHHT
T ss_pred             HHHHhhHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhc
Confidence            99999999999999998774  243 345555555555443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.81  E-value=0.00045  Score=47.70  Aligned_cols=91  Identities=10%  Similarity=0.010  Sum_probs=64.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HhhHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDA---YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD----SQTYTEVI  184 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~---~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li  184 (256)
                      +-..+...|++++|...|+...+..  +.+.   ..+..+-.+|...|++++|...|++..+..  |+    ...+..+-
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la   83 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLG   83 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHH
Confidence            3445667788888888888877664  2223   466667777888888888888888877632  33    45566677


Q ss_pred             HHHHHcCChhHHHHHHHHHHhC
Q 025225          185 RGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       185 ~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ..|.+.|++++|...|++..+.
T Consensus        84 ~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           84 LSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            7777888888888888887765

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.80  E-value=0.00062  Score=54.70  Aligned_cols=151  Identities=13%  Similarity=0.042  Sum_probs=112.2

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH-HHHHhc
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLI-IALART  155 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li-~~~~~~  155 (256)
                      ..-..+.+.|+.++|...+-+......-.++.. .+-..+...|++++|...+++..+..   |+........ ..+...
T Consensus       122 ~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~---p~~~~~~~~~~~~l~~~  198 (287)
T 3qou_A          122 QQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD---QDTRYQGLVAQIELLXQ  198 (287)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG---CSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh---cchHHHHHHHHHHHHhh
Confidence            334566789999999855543333222222233 47788899999999999999987664   5554333333 336677


Q ss_pred             CCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC-CChhHHHHHHHHhcCCCChHHHHH
Q 025225          156 GKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP-PEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~-p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++.++|.+.|++....  .| +...+..+-..|...|++++|.+.|.+..+..-. .+...+..+...|...|+.++|..
T Consensus       199 ~~~~~a~~~l~~al~~--~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~  276 (287)
T 3qou_A          199 AADTPEIQQLQQQVAE--NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALAS  276 (287)
T ss_dssp             HTSCHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHH
T ss_pred             cccCccHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHH
Confidence            8888899999988764  25 5788899999999999999999999999876322 236678999999999999888876

>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=97.79  E-value=0.00039  Score=57.32  Aligned_cols=118  Identities=8%  Similarity=-0.059  Sum_probs=83.5

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCC---------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPD---------------AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD  176 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---------------~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  176 (256)
                      +=..+.+.|++++|...|++..+..  ..+               ...|..+-.+|.+.|++++|.+.|++..+.. ..+
T Consensus       153 ~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~  229 (336)
T 1p5q_A          153 RGTVYFKEGKYKQALLQYKKIVSWL--EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNN  229 (336)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHh--hccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCc
Confidence            4555667788888888888777664  222               5778888888888888888888888777642 125


Q ss_pred             HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          177 SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       177 ~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ...|..+-.+|.+.|++++|...|++..+.. .-+...+..+-..+.+.|+.+++.+
T Consensus       230 ~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~  285 (336)
T 1p5q_A          230 EKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREK  285 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            6777777788888888888888888777652 1245566677777777777776633

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.78  E-value=0.0016  Score=56.28  Aligned_cols=137  Identities=9%  Similarity=-0.012  Sum_probs=95.2

Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHc-----CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC---C
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQ-----EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG---K  157 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g---~  157 (256)
                      .++.++|+. +++...+.+.......+-..+...     ++.++|...|.+..+.|    +...+..+-..|...|   +
T Consensus       272 ~~d~~~A~~-~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~----~~~a~~~lg~~y~~~g~~~~  346 (490)
T 2xm6_A          272 AKEPLKALE-WYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG----DATAQANLGAIYFRLGSEEE  346 (490)
T ss_dssp             SCCHHHHHH-HHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHSCCHHH
T ss_pred             CCCHHHHHH-HHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC----CHHHHHHHHHHHHhCCCccc
Confidence            677777774 444554444322222344455555     78888888888888776    4556666766776655   7


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC----CCChH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP----HPLLR  229 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~----~g~~~  229 (256)
                      .++|.+.|++..+.   .+...+..|-..|..    .++.++|.++|++..+.|   +...+..|-..|.+    .++.+
T Consensus       347 ~~~A~~~~~~a~~~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~~  420 (490)
T 2xm6_A          347 HKKAVEWFRKAAAK---GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERDYV  420 (490)
T ss_dssp             HHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             HHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCCHH
Confidence            88888888888775   366777777777877    788888888888888765   45566666666665    77888


Q ss_pred             HHHH
Q 025225          230 SKVK  233 (256)
Q Consensus       230 ~a~~  233 (256)
                      +|.+
T Consensus       421 ~A~~  424 (490)
T 2xm6_A          421 QAWA  424 (490)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8877

>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=97.77  E-value=0.00019  Score=49.34  Aligned_cols=107  Identities=8%  Similarity=0.073  Sum_probs=83.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCC--CCC----hhHH
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPD--PPE----ELPF  215 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~--~p~----~~t~  215 (256)
                      ...|..+-..+...|++++|...|++..+.. +.+...+..+-..|.+.|++++|...+++..+...  .++    ...|
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHH
Confidence            4567888889999999999999999988743 23677888999999999999999999999876521  223    6788


Q ss_pred             HHHHHHhcCCCChHHHHHh--hhhhcCCCcccccch
Q 025225          216 RILLKGLLPHPLLRSKVKK--DFEELFPEKHAYDPP  249 (256)
Q Consensus       216 ~~li~~~~~~g~~~~a~~~--~~~~~~p~~~~~~~l  249 (256)
                      ..+...|.+.|++++|.+.  ......|+......+
T Consensus        83 ~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l  118 (131)
T 1elr_A           83 ARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKC  118 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            8899999999999999982  223345654444433

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.75  E-value=0.00075  Score=47.08  Aligned_cols=96  Identities=11%  Similarity=-0.051  Sum_probs=75.0

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      ..=..|.+.|+.++|+..+-+......-.+... .+-.++.+.|++++|++.|+...+..  ..+...|..+-.+|...|
T Consensus        18 ~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~   95 (126)
T 4gco_A           18 NKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD--SKFIKGYIRKAACLVAMR   95 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh--hhhhHHHHHHHHHHHHCC
Confidence            344678899999999966544443332223333 46677889999999999999999886  678899999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCH
Q 025225          157 KMNEAMQVWESMRKEDLFPDS  177 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~  177 (256)
                      ++++|.+.|++..+.  .|+-
T Consensus        96 ~~~~A~~~~~~al~l--~P~~  114 (126)
T 4gco_A           96 EWSKAQRAYEDALQV--DPSN  114 (126)
T ss_dssp             CHHHHHHHHHHHHHH--CTTC
T ss_pred             CHHHHHHHHHHHHHH--CcCC
Confidence            999999999998873  4653

>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=97.75  E-value=0.00049  Score=55.77  Aligned_cols=151  Identities=10%  Similarity=0.042  Sum_probs=85.5

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhh---ccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCC--HHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVL---RLLKMDIV----AVLIELERQEETILAVKIFDIIRKQ----DWYQPD--AYIYK  146 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~--~~~y~  146 (256)
                      ...|...|++++|+..+.+....   .+-.+...    .+-..|.+.|++++|...|++..+.    |  .|.  ..+|+
T Consensus        43 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g--~~~~~a~~~~  120 (307)
T 2ifu_A           43 AVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENG--TPDTAAMALD  120 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTT--CHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcC--CHHHHHHHHH
Confidence            34556677777776544332221   11111111    2555566677777777777764432    2  121  34666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCCh-hHHH
Q 025225          147 DLIIALARTGKMNEAMQVWESMRKE----DLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPEE-LPFR  216 (256)
Q Consensus       147 ~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~~-~t~~  216 (256)
                      .+-..|.. |++++|.+.|++..+.    |-.+ ...+++.+-..|.+.|++++|.+.|++..+.    +..++. ..+.
T Consensus       121 ~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  199 (307)
T 2ifu_A          121 RAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCI  199 (307)
T ss_dssp             HHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHH
Confidence            66666766 7777777777766542    1000 1356667777777777777777777776542    222222 2455


Q ss_pred             HHHHHhcCCCChHHHHH
Q 025225          217 ILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       217 ~li~~~~~~g~~~~a~~  233 (256)
                      .+...+...|++++|..
T Consensus       200 ~~g~~~~~~g~~~~A~~  216 (307)
T 2ifu_A          200 AQVLVQLHRADYVAAQK  216 (307)
T ss_dssp             HHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHH
Confidence            55566666677777776

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.75  E-value=0.0016  Score=45.77  Aligned_cols=86  Identities=12%  Similarity=0.003  Sum_probs=43.8

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHH
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPD----AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLK  189 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~  189 (256)
                      .+...|++++|.+.|++..+..   |+    ...|..+-..|...|++++|.+.|++..+.  .| +...|..+-..|.+
T Consensus        37 ~~~~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~  111 (148)
T 2dba_A           37 ELFKCGDYGGALAAYTQALGLD---ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK--DGGDVKALYRRSQALEK  111 (148)
T ss_dssp             HHHTTTCHHHHHHHHHHHHTSC---CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TSCCHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHHc---ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CccCHHHHHHHHHHHHH
Confidence            3444555555555555554432   33    445555555555555555555555554442  12 34445555555555


Q ss_pred             cCChhHHHHHHHHHHh
Q 025225          190 DGSPADAMNIYEDMIK  205 (256)
Q Consensus       190 ~g~~~~a~~~~~~M~~  205 (256)
                      .|++++|...|++..+
T Consensus       112 ~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          112 LGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            5555555555555544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.73  E-value=0.00074  Score=56.27  Aligned_cols=158  Identities=9%  Similarity=-0.024  Sum_probs=107.1

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCc----HH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC----HH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMD----IV----AVLIELERQEETILAVKIFDIIRKQDWYQPD----AY  143 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~  143 (256)
                      +..+-..|...|+.++|+..+.+......-.++    ..    .+=..|...|++++|...|++..+...-.++    ..
T Consensus       146 ~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  225 (383)
T 3ulq_A          146 FFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGR  225 (383)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            344456778899999998555433322111122    11    2556777889999999999987644201122    24


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC----CC-CCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCChhH
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKE----DL-FPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPEELP  214 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~~~t  214 (256)
                      +|+.+-..|...|++++|.+.|++..+.    +- .....++..+-..|.+.|++++|.+.+++..+.    +-......
T Consensus       226 ~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  305 (383)
T 3ulq_A          226 TLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSE  305 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            7888889999999999999999988762    22 234577888999999999999999999887643    22222334


Q ss_pred             HHHHHHHhcCCCC---hHHHHH
Q 025225          215 FRILLKGLLPHPL---LRSKVK  233 (256)
Q Consensus       215 ~~~li~~~~~~g~---~~~a~~  233 (256)
                      +..+-..|...|+   +++|+.
T Consensus       306 ~~~l~~~~~~~~~~~~~~~al~  327 (383)
T 3ulq_A          306 FEFLKSLYLSGPDEEAIQGFFD  327 (383)
T ss_dssp             HHHHHHHHTSSCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHH
Confidence            5667777777777   555655

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.73  E-value=0.00075  Score=53.00  Aligned_cols=128  Identities=15%  Similarity=0.072  Sum_probs=96.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC-HhhHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPD---AYIYKDLIIALARTGKMNEAMQVWESMRKED-LFPD-SQTYTEVIR  185 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~-~~t~~~li~  185 (256)
                      .+-..+.+.|++++|...|++..+..  +-+   ...+..+-.+|.+.|++++|...|++..+.. -.|+ ...+..+-.
T Consensus        20 ~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~   97 (261)
T 3qky_A           20 ERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAM   97 (261)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHH
Confidence            45667788999999999999999875  233   6788889999999999999999999998742 1122 345666777


Q ss_pred             HHHH--------cCChhHHHHHHHHHHhCCCCCCh-hHH-----------------HHHHHHhcCCCChHHHHHhhh--h
Q 025225          186 GFLK--------DGSPADAMNIYEDMIKSPDPPEE-LPF-----------------RILLKGLLPHPLLRSKVKKDF--E  237 (256)
Q Consensus       186 ~~~~--------~g~~~~a~~~~~~M~~~g~~p~~-~t~-----------------~~li~~~~~~g~~~~a~~~~~--~  237 (256)
                      .|.+        .|++++|...|++..+..  |+. ...                 ..+-..|.+.|++++|+....  -
T Consensus        98 ~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l  175 (261)
T 3qky_A           98 CYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVF  175 (261)
T ss_dssp             HHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            7777        999999999999998752  322 223                 445778889999999999332  3


Q ss_pred             hcCCC
Q 025225          238 ELFPE  242 (256)
Q Consensus       238 ~~~p~  242 (256)
                      ...|+
T Consensus       176 ~~~p~  180 (261)
T 3qky_A          176 DAYPD  180 (261)
T ss_dssp             HHCTT
T ss_pred             HHCCC
Confidence            34565

>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=97.72  E-value=0.00018  Score=53.19  Aligned_cols=127  Identities=14%  Similarity=0.089  Sum_probs=89.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHH--HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIE--LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~--~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+..+-..+.+.|+.++|+..+ +......-.|....+...  +...++..+|...+++..+..  +-+...+..+-..+
T Consensus        42 a~~~la~~~~~~g~~~~A~~~~-~~a~~~~p~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~--P~~~~~~~~la~~~  118 (176)
T 2r5s_A           42 VKLAKADCLLETKQFELAQELL-ATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAAN--PDNFELACELAVQY  118 (176)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHH-TTCCGGGCCHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHS--TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHH-HHhhhccCChHHHHHHHHHHHHhhcccchHHHHHHHHHHhC--CCCHHHHHHHHHHH
Confidence            3445566788999999998544 443322212222222211  122223345788899888775  45789999999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      ...|++++|.+.|++..+..-.+ +...+..+...|...|+.++|...|++..
T Consensus       119 ~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A          119 NQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHH
Confidence            99999999999999998854222 35688999999999999999999998754

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.72  E-value=0.00056  Score=45.50  Aligned_cols=95  Identities=11%  Similarity=0.014  Sum_probs=78.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC-CChhHHHHHH
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP-PEELPFRILL  219 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~-p~~~t~~~li  219 (256)
                      +...|..+-..+...|++++|...|++..+.. ..+...|..+-..|.+.|++++|.+.|++..+.... .+...+..+.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~   83 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKA   83 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHH
Confidence            34567778888999999999999999988742 235678888999999999999999999999876321 1578889999


Q ss_pred             HHhcCC-CChHHHHHhhh
Q 025225          220 KGLLPH-PLLRSKVKKDF  236 (256)
Q Consensus       220 ~~~~~~-g~~~~a~~~~~  236 (256)
                      ..|.+. |++++|.+...
T Consensus        84 ~~~~~~~~~~~~A~~~~~  101 (112)
T 2kck_A           84 DALRYIEGKEVEAEIAEA  101 (112)
T ss_dssp             HHHTTCSSCSHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHH
Confidence            999999 99999999433

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.71  E-value=0.0023  Score=55.28  Aligned_cols=137  Identities=7%  Similarity=-0.008  Sum_probs=70.6

Q ss_pred             CCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHH----cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cCC
Q 025225           86 FKDDEEKLQKFIKTHVLRLLKMDIVAVLIELER----QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TGK  157 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g~  157 (256)
                      .++.++|+. +++.....+.......+-..|..    .++.++|++.|++..+.|    +...+..+-..|..    .++
T Consensus       128 ~~~~~~A~~-~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~----~~~a~~~Lg~~y~~g~g~~~~  202 (490)
T 2xm6_A          128 KVDKAESVK-WFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG----NVWSCNQLGYMYSRGLGVERN  202 (490)
T ss_dssp             CCCHHHHHH-HHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCC
T ss_pred             CCCHHHHHH-HHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHhcCCCCCcC
Confidence            556666653 33444444421111123333433    456666666666666554    45555556555655    566


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC----CCChH
Q 025225          158 MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLP----HPLLR  229 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~----~g~~~  229 (256)
                      .++|.+.|++..+.|   +...+..+-..|..    .++.++|.++|++..+.|   +...+..+-..|..    .++.+
T Consensus       203 ~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~  276 (490)
T 2xm6_A          203 DAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPL  276 (490)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHH
T ss_pred             HHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHH
Confidence            666666666665542   44455555555554    556666666666655543   22233333333333    45555


Q ss_pred             HHHH
Q 025225          230 SKVK  233 (256)
Q Consensus       230 ~a~~  233 (256)
                      +|++
T Consensus       277 ~A~~  280 (490)
T 2xm6_A          277 KALE  280 (490)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5555

>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=97.69  E-value=0.001  Score=63.99  Aligned_cols=136  Identities=18%  Similarity=0.148  Sum_probs=105.0

Q ss_pred             hhHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           74 KEALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      ..|..+-.++.+.|++++|++.+.+    .+- |+.+ .++.++.+.|++++|.+.+..-++..   +++...+.+.-+|
T Consensus      1106 ~vWsqLAKAql~~G~~kEAIdsYiK----AdD-~say~eVa~~~~~lGkyEEAIeyL~mArk~~---~e~~Idt~LafaY 1177 (1630)
T 1xi4_A         1106 AVWSQLAKAQLQKGMVKEAIDSYIK----ADD-PSSYMEVVQAANTSGNWEELVKYLQMARKKA---RESYVETELIFAL 1177 (1630)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHh----cCC-hHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc---ccccccHHHHHHH
Confidence            3566667788888999999876632    222 3333 58999999999999999998766553   4444455699999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ++.+++++...+.    .   .|+...|..+=..|-..|++++|..+|...         ..|..+..+|++.|++++|+
T Consensus      1178 AKl~rleele~fI----~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AI 1241 (1630)
T 1xi4_A         1178 AKTNRLAELEEFI----N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAV 1241 (1630)
T ss_pred             HhhcCHHHHHHHH----h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHH
Confidence            9999988655443    2   267777888888888999999999999984         58999999999999999999


Q ss_pred             H
Q 025225          233 K  233 (256)
Q Consensus       233 ~  233 (256)
                      +
T Consensus      1242 E 1242 (1630)
T 1xi4_A         1242 D 1242 (1630)
T ss_pred             H
Confidence            8

>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=97.68  E-value=0.00034  Score=63.36  Aligned_cols=145  Identities=12%  Similarity=0.044  Sum_probs=108.8

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+..+-..+.+.|+.++|+..+ +...+.. -.+... .+=.++...|++++|.+.|++..+..  .-+...|..+-.+|
T Consensus       435 ~~~~~a~~~~~~g~~~~A~~~~-~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~lg~~~  511 (681)
T 2pzi_A          435 LPLMEVRALLDLGDVAKATRKL-DDLAERVGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTF--PGELAPKLALAATA  511 (681)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHH-HHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHH-HHHhccCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHH
Confidence            4445566788899999998655 4443322 112222 35567888999999999999999886  55778899999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-hhHHHHHHHHhcCCCC
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-ELPFRILLKGLLPHPL  227 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-~~t~~~li~~~~~~g~  227 (256)
                      .+.|++++ .+.|++..+.  .| +...|..+-..|.+.|++++|.+.|++..+.  .|+ ...|..+..++...|.
T Consensus       512 ~~~g~~~~-~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          512 ELAGNTDE-HKFYQTVWST--NDGVISAAFGLARARSAEGDRVGAVRTLDEVPPT--SRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHTCCCT-TCHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTT--STTHHHHHHHHHHHTC----
T ss_pred             HHcCChHH-HHHHHHHHHh--CCchHHHHHHHHHHHHHcCCHHHHHHHHHhhccc--CcccHHHHHHHHHHHHccCC
Confidence            99999999 9999998874  24 5678999999999999999999999987665  454 4566677777776554

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.64  E-value=0.0002  Score=59.95  Aligned_cols=155  Identities=11%  Similarity=-0.026  Sum_probs=104.6

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccC-CCcH----H-HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLL-KMDI----V-AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAYIYKD  147 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~----~-~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~~y~~  147 (256)
                      ..-..+...|+.++|+..+ +......- .+..    . .+-..+...|++++|...|++..+.    +.......+|..
T Consensus        53 ~~g~~~~~~g~~~~A~~~~-~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  131 (411)
T 4a1s_A           53 LEGERLCNAGDCRAGVAFF-QAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGN  131 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHH-HHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHH-HHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHH
Confidence            3456678889999998544 44444321 1111    1 3566677889999999998877644    101234567788


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHhhHHHHHHHHHHcCC-----------------hhHHHHHHHHHHh
Q 025225          148 LIIALARTGKMNEAMQVWESMRKE----DLFP-DSQTYTEVIRGFLKDGS-----------------PADAMNIYEDMIK  205 (256)
Q Consensus       148 li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g~-----------------~~~a~~~~~~M~~  205 (256)
                      +-..|...|++++|.+.|++..+.    +-.| ...+|..+-..|...|+                 +++|.+.+++..+
T Consensus       132 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~  211 (411)
T 4a1s_A          132 LGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLK  211 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHH
Confidence            888888999999999998887653    1111 24577788888888888                 8888888877643


Q ss_pred             C----CCC-CChhHHHHHHHHhcCCCChHHHHH
Q 025225          206 S----PDP-PEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       206 ~----g~~-p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .    +-. .....+..+-..|...|++++|.+
T Consensus       212 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  244 (411)
T 4a1s_A          212 LMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIE  244 (411)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            2    211 123467777888888888888877

>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=97.63  E-value=0.00068  Score=50.94  Aligned_cols=119  Identities=10%  Similarity=-0.106  Sum_probs=71.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCC--------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPD--------------AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS  177 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~--------------~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  177 (256)
                      +-..+.+.|++++|...|++..+...-.|+              ...|..+-.+|.+.|++++|...+++..+.. ..+.
T Consensus        44 ~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~  122 (198)
T 2fbn_A           44 EGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNV  122 (198)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccH
Confidence            344556677777777777776654311111              2667777777777777777777777776631 1245


Q ss_pred             hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          178 QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       178 ~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      ..|..+-..|...|++++|.+.|++..+.. .-+...+..+-..+...++..++.
T Consensus       123 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          123 KALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHHH
Confidence            667777777777777777777777766542 113445555555555555444433

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.62  E-value=0.00031  Score=58.37  Aligned_cols=221  Identities=8%  Similarity=-0.190  Sum_probs=142.7

Q ss_pred             cccccCCchHHHHHHHHHhc----CCC-------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccc
Q 025225            5 LFSRSKIPILASIVLQNLTK----NPS-------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIG   73 (256)
Q Consensus         5 ~~~~~~~~~~A~~l~~~m~~----~~~-------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~   73 (256)
                      .+...|+.+.|.+.++...+    .+.       +..+-..+...++...+     +..+++..........   .....
T Consensus        56 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~al~~~~~~~~---~~~~~  127 (406)
T 3sf4_A           56 AYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEA-----IVCCQRHLDISRELND---KVGEA  127 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHHHHHTC---HHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHHHHhccc---ccchH
Confidence            35567888899888776422    111       44444455566777666     6666554432111100   00112


Q ss_pred             hhHHHHHHHhhcCCC--------------------cHHHHHHHHHHHh---hccCCCcHH----HHHHHHHHcCCHHHHH
Q 025225           74 KEALFVILGLKRFKD--------------------DEEKLQKFIKTHV---LRLLKMDIV----AVLIELERQEETILAV  126 (256)
Q Consensus        74 ~~~~~~i~~~~~~~~--------------------~~~a~~~~~~~~~---~~~~~~~~~----~li~~~~~~~~~~~a~  126 (256)
                      ..+..+-..+...|+                    .++|+..+.+...   ..+-.|...    .+-..+...|++++|.
T Consensus       128 ~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  207 (406)
T 3sf4_A          128 RALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAV  207 (406)
T ss_dssp             HHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHH
T ss_pred             HHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHH
Confidence            234444566677787                    7887744432221   122222221    3667788899999999


Q ss_pred             HHHHHHHhcCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC-HhhHHHHHHHHHHcCChhHHH
Q 025225          127 KIFDIIRKQDWYQPD----AYIYKDLIIALARTGKMNEAMQVWESMRKE----DLFPD-SQTYTEVIRGFLKDGSPADAM  197 (256)
Q Consensus       127 ~~~~~m~~~~~~~p~----~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~~~~~~g~~~~a~  197 (256)
                      ..+++..+...-.++    ..+|..+-..|...|++++|...+++..+.    +-.+. ..++..+-..|.+.|++++|.
T Consensus       208 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  287 (406)
T 3sf4_A          208 IAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAI  287 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHH
Confidence            999987654211222    348888999999999999999999987652    11111 567888999999999999999


Q ss_pred             HHHHHHHhC----CCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          198 NIYEDMIKS----PDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       198 ~~~~~M~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +.+++..+.    +-.+ ...++..+-..|...|++++|.+
T Consensus       288 ~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  328 (406)
T 3sf4_A          288 DYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMH  328 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            999987653    2111 15577888899999999999988

>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=97.60  E-value=0.0056  Score=40.77  Aligned_cols=93  Identities=11%  Similarity=-0.098  Sum_probs=71.8

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      +......+...|+.++|+..+ +...... -.+... .+-..+...|++++|...+++..+..  ..+...|..+-..|.
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~   83 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCY-SEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK--PDWGKGYSRKAAALE   83 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHH-HHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHH-HHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC--cccHHHHHHHHHHHH
Confidence            344556778899999998555 4443322 222222 36677888999999999999998886  557889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhC
Q 025225          154 RTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~  171 (256)
                      ..|++++|.+.|++..+.
T Consensus        84 ~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           84 FLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HTTCHHHHHHHHHHHHTT
T ss_pred             HHhhHHHHHHHHHHHHHc
Confidence            999999999999998874

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.59  E-value=0.00014  Score=49.96  Aligned_cols=86  Identities=14%  Similarity=0.045  Sum_probs=49.8

Q ss_pred             cCCHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHH
Q 025225          119 QEETILAVKIFDIIRKQDWY-QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADA  196 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~-~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a  196 (256)
                      .|++++|+..|++..+.+.- .-+...|..+-..|...|++++|.+.|++..+..  | +...+..+-..|.+.|++++|
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF--PNHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHcCCHHHH
Confidence            45666666677666654200 1234556666666667777777777777666532  3 355666666666677777777


Q ss_pred             HHHHHHHHhC
Q 025225          197 MNIYEDMIKS  206 (256)
Q Consensus       197 ~~~~~~M~~~  206 (256)
                      .+.|++..+.
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            7777665543

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.58  E-value=0.0018  Score=51.92  Aligned_cols=121  Identities=8%  Similarity=-0.002  Sum_probs=92.3

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCH------HHHHHHHHHHHhcCCHHHHHHHHHHHHhCC---CCCC--Hhh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDA------YIYKDLIIALARTGKMNEAMQVWESMRKED---LFPD--SQT  179 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~------~~y~~li~~~~~~g~~~~a~~~~~~m~~~g---~~p~--~~t  179 (256)
                      ..+..+...|++++|.+.+++..+..  ..+.      ..+..+...+...|++++|.+.|++..+..   ..+.  ..+
T Consensus        80 ~~~~~~~~~~~y~~A~~~~~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 2qfc_A           80 DQVIMLCKQKRYKEIYNKVWNELKKE--EYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTC--CCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHhccc--cCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            46778889999999999999887764  2222      223445556678899999999999887532   1222  458


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHhC----CCCC--ChhHHHHHHHHhcCCCChHHHHH
Q 025225          180 YTEVIRGFLKDGSPADAMNIYEDMIKS----PDPP--EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       180 ~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p--~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      |+.+-..|...|++++|.+.|++..+.    +-.+  ...+|..+-..|.+.|++++|++
T Consensus       158 ~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~  217 (293)
T 2qfc_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLY  217 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHH
Confidence            899999999999999999999988732    2112  22588899999999999999998

>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=97.56  E-value=0.0031  Score=51.87  Aligned_cols=126  Identities=8%  Similarity=-0.054  Sum_probs=97.0

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC---------------cHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCC
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM---------------DIV-AVLIELERQEETILAVKIFDIIRKQDWY  138 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~  138 (256)
                      .+..+-..+.+.|+.++|+..+.+......-.+               ... .+-.++.+.|++++|+..|++..+..  
T Consensus       149 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~--  226 (336)
T 1p5q_A          149 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD--  226 (336)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--
Confidence            334445677889999999865544333222211               111 36677889999999999999999886  


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHH-HHHHHHHH
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADA-MNIYEDMI  204 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a-~~~~~~M~  204 (256)
                      ..+...|..+-.+|...|++++|.+.|++..+.  .| +...+..+-..+.+.|+.++| ...|.+|.
T Consensus       227 p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          227 SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            668999999999999999999999999998874  34 567888888999999999988 55666664

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.56  E-value=0.00023  Score=59.58  Aligned_cols=159  Identities=8%  Similarity=-0.084  Sum_probs=110.9

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhh---ccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVL---RLLKMDIV----AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAY  143 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~  143 (256)
                      .+..+-..+...|+.++|...+.+....   .+-.|...    .+-..+...|++++|...|++..+.    +.......
T Consensus        88 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  167 (411)
T 4a1s_A           88 IYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGR  167 (411)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHH
Confidence            3445566778889999998544332221   11122222    3667778899999999999987654    10122356


Q ss_pred             HHHHHHHHHHhcCC-----------------HHHHHHHHHHHHhC----CCCC-CHhhHHHHHHHHHHcCChhHHHHHHH
Q 025225          144 IYKDLIIALARTGK-----------------MNEAMQVWESMRKE----DLFP-DSQTYTEVIRGFLKDGSPADAMNIYE  201 (256)
Q Consensus       144 ~y~~li~~~~~~g~-----------------~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~  201 (256)
                      +|..+-..|...|+                 +++|.+.+++..+.    +-.| ...+|..+-..|...|++++|.+.|+
T Consensus       168 ~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  247 (411)
T 4a1s_A          168 ALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQ  247 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            78888889999999                 99999999886542    1111 23578888889999999999999999


Q ss_pred             HHHhCCC-CCC----hhHHHHHHHHhcCCCChHHHHH
Q 025225          202 DMIKSPD-PPE----ELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       202 ~M~~~g~-~p~----~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +..+..- .++    ...+..+...|...|++++|.+
T Consensus       248 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  284 (411)
T 4a1s_A          248 ERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAE  284 (411)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHH
Confidence            8765311 111    2378889999999999999988

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.55  E-value=0.00051  Score=55.13  Aligned_cols=153  Identities=14%  Similarity=0.023  Sum_probs=82.6

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCC-CcH--H---HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHHHHHHHH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLK-MDI--V---AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAYIYKDLI  149 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~--~---~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~~y~~li  149 (256)
                      -..+...|+.++|+..+ +........ |..  .   .+-..+...|++++|.+.+++..+.    +.......++..+-
T Consensus        12 g~~~~~~g~~~~A~~~~-~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~   90 (338)
T 3ro2_A           12 GERLCKSGDCRAGVSFF-EAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLG   90 (338)
T ss_dssp             HHHHHHTTCHHHHHHHH-HHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHH-HHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHH
Confidence            34556677777776433 333332211 110  1   2455566677777777777664432    10011245566666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhC-CCCCC----HhhHHHHHHHHHHcCC--------------------hhHHHHHHHHHH
Q 025225          150 IALARTGKMNEAMQVWESMRKE-DLFPD----SQTYTEVIRGFLKDGS--------------------PADAMNIYEDMI  204 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~-g~~p~----~~t~~~li~~~~~~g~--------------------~~~a~~~~~~M~  204 (256)
                      ..|...|++++|.+.+++..+. .-.++    ..++..+-..|...|+                    +++|.+.+++..
T Consensus        91 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~  170 (338)
T 3ro2_A           91 NTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENL  170 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence            6777777777777777765442 00112    2356666666666777                    677776666544


Q ss_pred             hC----CCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          205 KS----PDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       205 ~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +.    +-.| ....+..+...|...|++++|.+
T Consensus       171 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  204 (338)
T 3ro2_A          171 SLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVI  204 (338)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            21    1111 12355566666666777776666

>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=97.54  E-value=0.0071  Score=46.00  Aligned_cols=147  Identities=5%  Similarity=-0.101  Sum_probs=105.5

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcC----CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQE----ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~----~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      +-..|...++.++|+. +++.....|.......|=..|.. +    +.++|.+.|....+.|    ++..+..|-..|..
T Consensus        24 lg~~~~~~~~~~~A~~-~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g----~~~a~~~Lg~~y~~   97 (212)
T 3rjv_A           24 LADTWVSSGDYQKAEY-WAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG----SKSGEIVLARVLVN   97 (212)
T ss_dssp             HHHHHHHHTCHHHHHH-HHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHTC
T ss_pred             HHHHHhcCCCHHHHHH-HHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHc
Confidence            3445566899999984 55566555542222233333444 6    8999999999998777    67778888888877


Q ss_pred             ----cCCHHHHHHHHHHHHhCCCC-CCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC
Q 025225          155 ----TGKMNEAMQVWESMRKEDLF-PDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH  225 (256)
Q Consensus       155 ----~g~~~~a~~~~~~m~~~g~~-p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~  225 (256)
                          .+++++|.+.|++..+.|-. .+...+..|=..|..    .++.++|..+|++-.+.+  ++...+..|-..|...
T Consensus        98 g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~--~~~~a~~~Lg~~y~~g  175 (212)
T 3rjv_A           98 RQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLS--RTGYAEYWAGMMFQQG  175 (212)
T ss_dssp             GGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS--CTTHHHHHHHHHHHHC
T ss_pred             CCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHcC
Confidence                88999999999998876421 026788888888888    789999999999998772  2444566666666532


Q ss_pred             ------CChHHHHH
Q 025225          226 ------PLLRSKVK  233 (256)
Q Consensus       226 ------g~~~~a~~  233 (256)
                            .+.++|.+
T Consensus       176 ~gg~~~~d~~~A~~  189 (212)
T 3rjv_A          176 EKGFIEPNKQKALH  189 (212)
T ss_dssp             BTTTBCCCHHHHHH
T ss_pred             CCCCCCCCHHHHHH
Confidence                  37888887

>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=97.54  E-value=0.0016  Score=45.25  Aligned_cols=93  Identities=16%  Similarity=0.049  Sum_probs=80.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHH
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIL  218 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~l  218 (256)
                      ..+...|..+-..+...|++++|...|++..+.. +.+...|..+-..|.+.|++++|...|++..+.. +.+...|..+
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l   83 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFL   83 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHH
Confidence            4578899999999999999999999999988743 2357889999999999999999999999988753 2256788899


Q ss_pred             HHHhcCCCChHHHHH
Q 025225          219 LKGLLPHPLLRSKVK  233 (256)
Q Consensus       219 i~~~~~~g~~~~a~~  233 (256)
                      -..|...|++++|.+
T Consensus        84 ~~~~~~~~~~~~A~~   98 (137)
T 3q49_B           84 GQCQLEMESYDEAIA   98 (137)
T ss_dssp             HHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhhHHHHHH
Confidence            999999999999988

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.54  E-value=0.0017  Score=45.66  Aligned_cols=101  Identities=12%  Similarity=-0.057  Sum_probs=82.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhH
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD----SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELP  214 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t  214 (256)
                      ..+...+..+-..+...|++++|.+.|++..+.  .|+    ...|..+-..|.+.|++++|.+.+++..+.. ..+...
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  101 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKA  101 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHH
Confidence            356788999999999999999999999998874  466    6888889999999999999999999987652 225677


Q ss_pred             HHHHHHHhcCCCChHHHHHhhh--hhcCCC
Q 025225          215 FRILLKGLLPHPLLRSKVKKDF--EELFPE  242 (256)
Q Consensus       215 ~~~li~~~~~~g~~~~a~~~~~--~~~~p~  242 (256)
                      |..+-..|...|++++|.+...  ..+.|+
T Consensus       102 ~~~~a~~~~~~~~~~~A~~~~~~al~~~p~  131 (148)
T 2dba_A          102 LYRRSQALEKLGRLDQAVLDLQRCVSLEPK  131 (148)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCC
Confidence            8888899999999999988333  334454

>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=97.52  E-value=0.00045  Score=59.89  Aligned_cols=112  Identities=13%  Similarity=0.063  Sum_probs=59.7

Q ss_pred             HHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhH
Q 025225          117 ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPAD  195 (256)
Q Consensus       117 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~  195 (256)
                      .+.|++++|.+.|++..+..  .-+..+|..+-.+|.+.|++++|.+.|++..+.  .| +...|..+-..|.+.|++++
T Consensus        17 ~~~g~~~~A~~~~~~Al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~g~~~e   92 (477)
T 1wao_1           17 FKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFRA   92 (477)
T ss_dssp             TTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHhCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHH
Confidence            34556666666666665553  344566666666666666666666666666553  23 34555566666666666666


Q ss_pred             HHHHHHHHHhCCCCCChhHHHHHHHH--hcCCCChHHHHH
Q 025225          196 AMNIYEDMIKSPDPPEELPFRILLKG--LLPHPLLRSKVK  233 (256)
Q Consensus       196 a~~~~~~M~~~g~~p~~~t~~~li~~--~~~~g~~~~a~~  233 (256)
                      |.+.|++..+..-. +...+..+-.+  +.+.|++++|++
T Consensus        93 A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~g~~~~A~~  131 (477)
T 1wao_1           93 ALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIA  131 (477)
T ss_dssp             HHHHHHHHHHHSTT-CTTHHHHHHHHHHHHHHHHHCCC--
T ss_pred             HHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            66666665543110 12223333333  455555555555

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.51  E-value=0.007  Score=50.22  Aligned_cols=156  Identities=9%  Similarity=0.006  Sum_probs=108.7

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccC----CCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLL----KMDIV----AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAYI  144 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~~  144 (256)
                      ..+-..|...|+.++|+..+.+......-    .+...    .+=..|...|++++|.+.|++..+.    +.......+
T Consensus       145 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  224 (378)
T 3q15_A          145 FKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAIS  224 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            34456778899999998555433322111    12111    3566678899999999999987653    201112457


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCChhHH
Q 025225          145 YKDLIIALARTGKMNEAMQVWESMRK-----EDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPEELPF  215 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~~~t~  215 (256)
                      ++.+-..|...|++++|.+.|++..+     .. .....++..+-..|.+.|++++|.+.+++..+.    +-......+
T Consensus       225 ~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  303 (378)
T 3q15_A          225 LLNIANSYDRSGDDQMAVEHFQKAAKVSREKVP-DLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELF  303 (378)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCG-GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            88888899999999999999998876     32 223677888999999999999999999988753    222334456


Q ss_pred             HHHHHHhcCCCC---hHHHHH
Q 025225          216 RILLKGLLPHPL---LRSKVK  233 (256)
Q Consensus       216 ~~li~~~~~~g~---~~~a~~  233 (256)
                      +.+-..|...|+   +.+|+.
T Consensus       304 ~~l~~ly~~~~~~~~~~~al~  324 (378)
T 3q15_A          304 LFLQAVYKETVDERKIHDLLS  324 (378)
T ss_dssp             HHHHHHHSSSCCHHHHHHHHH
T ss_pred             HHHHHHHhCCCcHHHHHHHHH
Confidence            666667777777   666666

>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=97.50  E-value=0.002  Score=49.10  Aligned_cols=149  Identities=10%  Similarity=-0.112  Sum_probs=105.2

Q ss_pred             HHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC----CHHHHHHHHHHHHhCC
Q 025225           97 IKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG----KMNEAMQVWESMRKED  172 (256)
Q Consensus        97 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g----~~~~a~~~~~~m~~~g  172 (256)
                      ++...+.|.......+=..+...+++++|++.|+...+.|    ++..+..|=..|.. +    +.++|.+.|++..+.|
T Consensus         9 ~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g----~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g   83 (212)
T 3rjv_A            9 YQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG----DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG   83 (212)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT----CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC----CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC
Confidence            3444444442223345566667899999999999999887    56777777777777 6    8999999999998864


Q ss_pred             CCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCCC-CChhHHHHHHHHhcC----CCChHHHHHhhhhhc--CC
Q 025225          173 LFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPDP-PEELPFRILLKGLLP----HPLLRSKVKKDFEEL--FP  241 (256)
Q Consensus       173 ~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~~-p~~~t~~~li~~~~~----~g~~~~a~~~~~~~~--~p  241 (256)
                         +...+..|=..|..    .+++++|.++|++..+.|.. .+...+..|-..|..    .++.++|++...+.+  .+
T Consensus        84 ---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~  160 (212)
T 3rjv_A           84 ---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLSR  160 (212)
T ss_dssp             ---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTSC
T ss_pred             ---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcCC
Confidence               66777777777776    78999999999999887642 125666667677766    778999988333222  23


Q ss_pred             CcccccchhHhh
Q 025225          242 EKHAYDPPEEIF  253 (256)
Q Consensus       242 ~~~~~~~li~~y  253 (256)
                      +...+..|-.+|
T Consensus       161 ~~~a~~~Lg~~y  172 (212)
T 3rjv_A          161 TGYAEYWAGMMF  172 (212)
T ss_dssp             TTHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            444444444444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.50  E-value=0.0015  Score=47.25  Aligned_cols=93  Identities=11%  Similarity=0.072  Sum_probs=61.3

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhc--------CC--------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 025225          113 LIELERQEETILAVKIFDIIRKQ--------DW--------YQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD  176 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~--------~~--------~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  176 (256)
                      =..+.+.|++++|...|.+..+.        ..        -..+...|..+-.+|.+.|++++|...+++..+.. +.+
T Consensus        18 G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~   96 (162)
T 3rkv_A           18 GNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETN   96 (162)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-Ccc
Confidence            34455666777777777665544        00        01234567777777778888888888887776632 124


Q ss_pred             HhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          177 SQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       177 ~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ...|..+-.+|...|++++|...|++..+.
T Consensus        97 ~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           97 EKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            567777777777888888888888776655

>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=97.50  E-value=0.0061  Score=41.78  Aligned_cols=93  Identities=9%  Similarity=-0.076  Sum_probs=72.3

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART  155 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~  155 (256)
                      ...-..+.+.|+.++|+..+.+......-.+... .+-.++.+.|++++|...|++..+..  .-+...|..+-.+|...
T Consensus         8 ~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~   85 (126)
T 3upv_A            8 RLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD--PNFVRAYIRKATAQIAV   85 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHH
Confidence            3445667889999999865544333322222222 47777889999999999999999886  56788999999999999


Q ss_pred             CCHHHHHHHHHHHHhC
Q 025225          156 GKMNEAMQVWESMRKE  171 (256)
Q Consensus       156 g~~~~a~~~~~~m~~~  171 (256)
                      |++++|.+.|++..+.
T Consensus        86 ~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           86 KEYASALETLDAARTK  101 (126)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             hCHHHHHHHHHHHHHh
Confidence            9999999999998763

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.48  E-value=0.00044  Score=59.08  Aligned_cols=47  Identities=13%  Similarity=-0.038  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          123 ILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       123 ~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      ++|...|+...+..  ..+..+|..+-..|...|++++|.+.|++..+.
T Consensus       317 ~~A~~~~~~a~~~~--~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~  363 (472)
T 4g1t_A          317 GHAVAHLKKADEAN--DNLFRVCSILASLHALADQYEEAEYYFQKEFSK  363 (472)
T ss_dssp             HHHHHHHHHHHHHC--TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhhcC--CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhc
Confidence            44444444444443  233344455555555556666666666555543

>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=97.46  E-value=0.0038  Score=46.70  Aligned_cols=127  Identities=10%  Similarity=-0.040  Sum_probs=87.1

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC----------------cHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCC
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM----------------DIV-AVLIELERQEETILAVKIFDIIRKQDWY  138 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~----------------~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~  138 (256)
                      +...-..+.+.|++++|+..+.+......-.|                ... .+-.++.+.|++++|+..++...+..  
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--  118 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID--  118 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--
Confidence            33445667789999999865544343222222                122 36667788999999999999999886  


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHH-HHHHHHHhC
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAM-NIYEDMIKS  206 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~-~~~~~M~~~  206 (256)
                      ..+...|..+-.+|...|++++|.+.|++..+.  .| +...+..+-..+...++.+++. ..|..|...
T Consensus       119 p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~  186 (198)
T 2fbn_A          119 KNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELCVNKLKEARKKDKLTFGGMFDK  186 (198)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHC------------
T ss_pred             cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            668899999999999999999999999998774  34 4567777777777777777666 555655544

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.45  E-value=0.013  Score=48.35  Aligned_cols=218  Identities=10%  Similarity=-0.088  Sum_probs=132.1

Q ss_pred             cccCCchHHHHHHHHHhcC-CC---------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhH
Q 025225            7 SRSKIPILASIVLQNLTKN-PS---------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEA   76 (256)
Q Consensus         7 ~~~~~~~~A~~l~~~m~~~-~~---------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~   76 (256)
                      ...|+++.|.+.++..... +.         ++.+-..+...++...+     ...+++............   ......
T Consensus        25 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~~~~~~~~~~---~~~~~~   96 (373)
T 1hz4_A           25 INDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRS-----LALMQQTEQMARQHDVWH---YALWSL   96 (373)
T ss_dssp             HHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHHHHHHTTCHH---HHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHH-----HHHHHHHHHHHHhcCcHH---HHHHHH
Confidence            4578888898888874332 11         11122233344555555     666654433211110000   001112


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhh---ccCC--CcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCC----CCHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVL---RLLK--MDIV----AVLIELERQEETILAVKIFDIIRKQDWYQ----PDAY  143 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~---~~~~--~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~----p~~~  143 (256)
                      ..+-..+...|++++|...+.+....   .+..  |...    .+-..+...|++++|...+++..+.. -.    ....
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~  175 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVL-SSYQPQQQLQ  175 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTSCGGGGHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh-hccCcHHHHH
Confidence            33445677899999998554333221   2222  3222    25566788999999999999877553 11    1346


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-hhHH-----HHHHHHHHcCChhHHHHHHHHHHhCCCCCC---hhH
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS-QTYT-----EVIRGFLKDGSPADAMNIYEDMIKSPDPPE---ELP  214 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~-----~li~~~~~~g~~~~a~~~~~~M~~~g~~p~---~~t  214 (256)
                      +|..+-..+...|++++|...+++.....-.++. ..+.     .....+...|++++|...+++..+....+.   ...
T Consensus       176 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  255 (373)
T 1hz4_A          176 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  255 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHH
Confidence            7888888999999999999999988753111111 1222     233447799999999999998876532221   235


Q ss_pred             HHHHHHHhcCCCChHHHHH
Q 025225          215 FRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       215 ~~~li~~~~~~g~~~~a~~  233 (256)
                      +..+...+...|++++|..
T Consensus       256 ~~~la~~~~~~g~~~~A~~  274 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPAEI  274 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHH
Confidence            6778888999999999887

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.45  E-value=0.0028  Score=45.79  Aligned_cols=100  Identities=11%  Similarity=0.005  Sum_probs=75.9

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+..+-..+.+.|+.++|+..+-+......-.|+.. .+=.++...|++++|...|++..+..  +-++..|..+-.+|.
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~--P~~~~~~~~lg~~~~  115 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG--KNDYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--SSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHH
Confidence            334445677899999999865543333222222222 46678889999999999999999886  557788999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHh
Q 025225          154 RTGKMNEAMQVWESMRKEDLFPDSQ  178 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~g~~p~~~  178 (256)
                      +.|++++|.+.|++..+.  .||..
T Consensus       116 ~lg~~~eA~~~~~~al~l--~~~~~  138 (151)
T 3gyz_A          116 RLKAPLKAKECFELVIQH--SNDEK  138 (151)
T ss_dssp             HTTCHHHHHHHHHHHHHH--CCCHH
T ss_pred             HcCCHHHHHHHHHHHHHh--CCCHH
Confidence            999999999999998884  36653

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.43  E-value=0.006  Score=44.08  Aligned_cols=95  Identities=7%  Similarity=-0.057  Sum_probs=74.3

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALA  153 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~  153 (256)
                      .+..+-..+.+.|++++|+..+.+......-.+... .+-.++.+.|++++|+..|++..+..  .-+...|..+-.+|.
T Consensus        13 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~   90 (164)
T 3sz7_A           13 KLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVD--PKYSKAWSRLGLARF   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHH
Confidence            344456678899999999865544343322222222 47777889999999999999999886  567899999999999


Q ss_pred             hcCCHHHHHHHHHHHHhC
Q 025225          154 RTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~  171 (256)
                      ..|++++|.+.|++..+.
T Consensus        91 ~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           91 DMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HccCHHHHHHHHHHHHHh
Confidence            999999999999998873

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.42  E-value=0.00053  Score=51.22  Aligned_cols=115  Identities=11%  Similarity=0.007  Sum_probs=86.3

Q ss_pred             HHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHhhHHHHHHHHHHcC
Q 025225          117 ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE----DLFP-DSQTYTEVIRGFLKDG  191 (256)
Q Consensus       117 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g  191 (256)
                      ...|++++|.++++.+...  ......+++.+-..|...|++++|.+.|++..+.    +..| ....++.+-..|...|
T Consensus         3 ~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   80 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH--PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAG   80 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS--TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             cccccHHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcC
Confidence            4679999999966666543  2456789999999999999999999999988762    2222 3467888888899999


Q ss_pred             ChhHHHHHHHHHHhC----CCCC--ChhHHHHHHHHhcCCCChHHHHH
Q 025225          192 SPADAMNIYEDMIKS----PDPP--EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~----g~~p--~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ++++|.+.+++..+.    +-.|  ....+..+-..+...|++++|.+
T Consensus        81 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~  128 (203)
T 3gw4_A           81 NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQ  128 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            999999999987643    2122  24557788888999999999988

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.40  E-value=0.0041  Score=43.90  Aligned_cols=92  Identities=9%  Similarity=-0.068  Sum_probs=70.7

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      ..-..+.+.|+.++|+..+.+......-.+... .+-.++...|++++|...|+...+..  +-+...|..+-.+|...|
T Consensus        23 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g  100 (142)
T 2xcb_A           23 ALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD--INEPRFPFHAAECHLQLG  100 (142)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CCCcHHHHHHHHHHHHcC
Confidence            345667889999999865543333222222222 46677889999999999999999886  567788889999999999


Q ss_pred             CHHHHHHHHHHHHhC
Q 025225          157 KMNEAMQVWESMRKE  171 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~  171 (256)
                      ++++|.+.|++..+.
T Consensus       101 ~~~~A~~~~~~al~~  115 (142)
T 2xcb_A          101 DLDGAESGFYSARAL  115 (142)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999998763

>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=97.40  E-value=0.0052  Score=49.61  Aligned_cols=154  Identities=14%  Similarity=0.036  Sum_probs=99.4

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhh---ccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCC--CC--CHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVL---RLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWY--QP--DAY  143 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~--~p--~~~  143 (256)
                      .+..+-..|.+.|++++|+..+.+....   .|-.....    .+-..|.. |++++|++.|++..+...-  .+  ...
T Consensus        78 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~  156 (307)
T 2ifu_A           78 AFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAE  156 (307)
T ss_dssp             HHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHH
Confidence            3344456777889999998555332221   12111111    24455666 9999999999987654200  11  156


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCCH-hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCCh------
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKE----DLFPDS-QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEE------  212 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~------  212 (256)
                      +|+.+-..|.+.|++++|.+.|++..+.    +..++. ..+..+...+...|++++|...|++.. .  .|+.      
T Consensus       157 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~--~p~~~~~~e~  233 (307)
T 2ifu_A          157 LIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-S--IPGFSGSEDC  233 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-T--STTSTTSHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-C--CCCCCCCHHH
Confidence            8889999999999999999999988762    222222 366777777888899999999999987 3  3321      


Q ss_pred             hHHHHHHHHhcCCCChHHHHH
Q 025225          213 LPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       213 ~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .....++..+ ..|+.+...+
T Consensus       234 ~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          234 AALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             HHHHHHHHHH-HTTCHHHHHH
T ss_pred             HHHHHHHHHH-HhcCHHHHHH
Confidence            2345566666 4566544433

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.38  E-value=0.004  Score=44.02  Aligned_cols=126  Identities=9%  Similarity=-0.112  Sum_probs=64.2

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC----HHHHHH
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQDWYQPD----AYIYKD  147 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~~  147 (256)
                      +-..+...|+.++|+..+.+......-.++..       .+-..+...|++++|...+++..+...-.++    ...+..
T Consensus        15 l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   94 (164)
T 3ro3_A           15 LGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYS   94 (164)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHH
Confidence            34455566777776643322221111111111       2445555667777777777665433100111    345556


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          148 LIIALARTGKMNEAMQVWESMRKE----DLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       148 li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +-..|...|++++|.+.+++..+.    +-.+ ...++..+-..|...|++++|.+.+++..
T Consensus        95 l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  156 (164)
T 3ro3_A           95 LGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  156 (164)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            666666667777777766665432    1111 12345556666666677777766666544

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.38  E-value=0.0075  Score=49.71  Aligned_cols=160  Identities=11%  Similarity=-0.107  Sum_probs=104.7

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-------HHHHHHHHcCCHHHHHHHHHHHHhc----CCCC--C-CHHH
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-------AVLIELERQEETILAVKIFDIIRKQ----DWYQ--P-DAYI  144 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~li~~~~~~~~~~~a~~~~~~m~~~----~~~~--p-~~~~  144 (256)
                      +-..+...|+.++|...+.+......-..+..       .+-..+...|++++|...+++..+.    + -.  | ...+
T Consensus        59 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~  137 (373)
T 1hz4_A           59 LGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQH-LEQLPMHEFL  137 (373)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT-CTTSTHHHHH
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc-cccCcHHHHH
Confidence            34556778999998754433222111111221       2556677899999999999987643    2 11  3 2456


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCC--CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCCh-hHHH---
Q 025225          145 YKDLIIALARTGKMNEAMQVWESMRKED--LFP--DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEE-LPFR---  216 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~-~t~~---  216 (256)
                      +..+-..|...|++++|...+++.....  ..+  ...+|..+-..+...|++++|.+.+++..+..-.++. ..+.   
T Consensus       138 ~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~  217 (373)
T 1hz4_A          138 VRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNA  217 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHH
Confidence            6778888999999999999999887532  111  2356778888899999999999999988653211111 1222   


Q ss_pred             --HHHHHhcCCCChHHHHHhhhhhc
Q 025225          217 --ILLKGLLPHPLLRSKVKKDFEEL  239 (256)
Q Consensus       217 --~li~~~~~~g~~~~a~~~~~~~~  239 (256)
                        ..+..+...|++++|........
T Consensus       218 ~~~~~~~~~~~g~~~~A~~~~~~a~  242 (373)
T 1hz4_A          218 NKVRVIYWQMTGDKAAAANWLRHTA  242 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHhCC
Confidence              23344778999999988444333

>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=97.37  E-value=0.0023  Score=54.97  Aligned_cols=118  Identities=8%  Similarity=-0.038  Sum_probs=84.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCC---------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPD---------------AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD  176 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---------------~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  176 (256)
                      +=..+.+.|++++|...|++..+..  ..+               ...|..+-.+|.+.|++++|...|++..+.. ..+
T Consensus       274 ~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~  350 (457)
T 1kt0_A          274 KGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SAN  350 (457)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTC
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-Ccc
Confidence            4456677888888888888877654  222               5788888888888888888888888877642 125


Q ss_pred             HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          177 SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       177 ~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ...|..+-.+|.+.|++++|...|++..+..- -+...+..+-..+.+.|+.+++.+
T Consensus       351 ~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~~~~~~~~~~a~~  406 (457)
T 1kt0_A          351 EKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP-QNKAARLQISMCQKKAKEHNERDR  406 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHH
Confidence            67778888888888888888888888776521 234566667777777777666654

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.36  E-value=0.012  Score=45.06  Aligned_cols=130  Identities=12%  Similarity=0.060  Sum_probs=90.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-H---HHHHHH------------------HcCCHHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-A---VLIELE------------------RQEETILAVKIFDII  132 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~---li~~~~------------------~~~~~~~a~~~~~~m  132 (256)
                      .+..+...+.+.|+.++|+..+-+......-.+... +   +-.++.                  ..|+.++|...|++.
T Consensus        43 a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  122 (225)
T 2yhc_A           43 VQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKL  122 (225)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHH
Confidence            344556778899999999966644343332223321 1   222222                  257899999999999


Q ss_pred             HhcCCCCCCHHHHH-----------------HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----hhHHHHHHHHHHcC
Q 025225          133 RKQDWYQPDAYIYK-----------------DLIIALARTGKMNEAMQVWESMRKEDLFPDS----QTYTEVIRGFLKDG  191 (256)
Q Consensus       133 ~~~~~~~p~~~~y~-----------------~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~g  191 (256)
                      .+..  +-+...+.                 .+-..|.+.|++++|...|++..+.  .|+.    ..+..+..+|.+.|
T Consensus       123 l~~~--P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g  198 (225)
T 2yhc_A          123 VRGY--PNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRD--YPDTQATRDALPLMENAYRQMQ  198 (225)
T ss_dssp             HTTC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTT
T ss_pred             HHHC--cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHH--CcCCCccHHHHHHHHHHHHHcC
Confidence            9774  22222332                 3445678899999999999998874  2543    46888999999999


Q ss_pred             ChhHHHHHHHHHHhCCC
Q 025225          192 SPADAMNIYEDMIKSPD  208 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~  208 (256)
                      +.++|.+.++.+...+.
T Consensus       199 ~~~~A~~~~~~l~~~~~  215 (225)
T 2yhc_A          199 MNAQAEKVAKIIAANSS  215 (225)
T ss_dssp             CHHHHHHHHHHHHHCCS
T ss_pred             CcHHHHHHHHHHHhhCC
Confidence            99999999999987743

>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=97.36  E-value=0.0013  Score=55.03  Aligned_cols=116  Identities=10%  Similarity=0.023  Sum_probs=91.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHh----------------cCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 025225          112 VLIELERQEETILAVKIFDIIRK----------------QDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP  175 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~----------------~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  175 (256)
                      +=..+.+.|++++|.+.|++..+                ..  .-+..+|..+-.+|.+.|++++|.+.+++..+.  .|
T Consensus       229 ~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~--~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--~p  304 (370)
T 1ihg_A          229 IGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQ--PVALSCVLNIGACKLKMSDWQGAVDSCLEALEI--DP  304 (370)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGH--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CT
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHH--HHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh--Cc
Confidence            45567788999999999998776                22  345678888999999999999999999998874  34


Q ss_pred             -CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          176 -DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       176 -~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                       +...|..+-.+|.+.|++++|.+.|++..+.  .| +...+..+-..+...++.+++.+
T Consensus       305 ~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          305 SNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence             5678888889999999999999999988765  23 45566667777777777666655

>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=97.36  E-value=0.0039  Score=49.82  Aligned_cols=91  Identities=9%  Similarity=-0.171  Sum_probs=61.5

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      ..-..+.+.|+.++|+..+.+......-.+... .+-.++.+.|++++|...+++..+..  .-+...|..+-.+|...|
T Consensus         9 ~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g   86 (281)
T 2c2l_A            9 EQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD--GQSVKAHFFLGQCQLEME   86 (281)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC--TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcC
Confidence            344566778888888754433333222222222 35666777888888888888877765  456777888888888888


Q ss_pred             CHHHHHHHHHHHHh
Q 025225          157 KMNEAMQVWESMRK  170 (256)
Q Consensus       157 ~~~~a~~~~~~m~~  170 (256)
                      ++++|...|++..+
T Consensus        87 ~~~~A~~~~~~al~  100 (281)
T 2c2l_A           87 SYDEAIANLQRAYS  100 (281)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            88888888887765

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.36  E-value=0.0081  Score=45.47  Aligned_cols=133  Identities=11%  Similarity=-0.003  Sum_probs=88.8

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      +-..+.+.|+.++|+..+-+......-.++.. .+-..+...|++++|...|++..+..  +-+..+|..+-..|...|+
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~  137 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE--ADNLAANIFLGNYYYLTAE  137 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHHhH
Confidence            45677899999999865543333222222222 47777889999999999999999886  5678889888888866654


Q ss_pred             --HHHHHHHHHHHHhCCCCCCHhh--HHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHH
Q 025225          158 --MNEAMQVWESMRKEDLFPDSQT--YTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILL  219 (256)
Q Consensus       158 --~~~a~~~~~~m~~~g~~p~~~t--~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li  219 (256)
                        .+.+...++....    |+...  +...-.++...|++++|...|++..+.  .|+......+.
T Consensus       138 ~~~~~~~~~~~~~~~----~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~~~~l~  197 (208)
T 3urz_A          138 QEKKKLETDYKKLSS----PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEAQKTLD  197 (208)
T ss_dssp             HHHHHHHHHHC---C----CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC----CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHHHHHHH
Confidence              4455666665543    55433  333334455678999999999998865  57755444433

>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=97.35  E-value=0.0022  Score=55.51  Aligned_cols=145  Identities=14%  Similarity=0.015  Sum_probs=97.3

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNE  160 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~  160 (256)
                      .+.+.|+.++|+..+.+......-.+... .+-.++.+.|++++|.+.+++..+..  .-+..+|..+-.+|...|++++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~lg~~~~~~g~~~e   92 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--KKYIKGYYRRAASNMALGKFRA   92 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHH
Confidence            34678999999865543333222112222 46777889999999999999999886  5678899999999999999999


Q ss_pred             HHHHHHHHHhCCCCCC-HhhHHHHHHH--HHHcCChhHHHHHHH-----------HHHhC-----CC-----CCChhHHH
Q 025225          161 AMQVWESMRKEDLFPD-SQTYTEVIRG--FLKDGSPADAMNIYE-----------DMIKS-----PD-----PPEELPFR  216 (256)
Q Consensus       161 a~~~~~~m~~~g~~p~-~~t~~~li~~--~~~~g~~~~a~~~~~-----------~M~~~-----g~-----~p~~~t~~  216 (256)
                      |.+.|++..+.  .|+ ...+..+-.+  +.+.|++++|.+.++           +-.+.     |.     ..+.....
T Consensus        93 A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~itl~~l~  170 (477)
T 1wao_1           93 ALRDYETVVKV--KPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRSVVDSLDIESMTIEDEYSGPKLEDGKVTISFMK  170 (477)
T ss_dssp             HHHHHHHHHHH--STTCTTHHHHHHHHHHHHHHHHHCCC------CCSTTTCCTTSSCCCCTTCCSCCCGGGSCCHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHhccccccchhHhhhhhhhccccccccccccccccccHHHHH
Confidence            99999998874  243 3445555444  888899999999998           22211     11     12445566


Q ss_pred             HHHHHhcCCCChHH
Q 025225          217 ILLKGLLPHPLLRS  230 (256)
Q Consensus       217 ~li~~~~~~g~~~~  230 (256)
                      .++..+.+.+.+.+
T Consensus       171 ~lie~l~~~~~l~e  184 (477)
T 1wao_1          171 ELMQWYKDQKKLHR  184 (477)
T ss_dssp             HHHHHHHTCCCCCH
T ss_pred             HHHHHHHcCCCCCH
Confidence            77777777665443

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.30  E-value=0.0064  Score=51.73  Aligned_cols=145  Identities=8%  Similarity=-0.017  Sum_probs=93.9

Q ss_pred             cCCCcHHHHHHHHHHHhhc-cCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc-------
Q 025225           85 RFKDDEEKLQKFIKTHVLR-LLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART-------  155 (256)
Q Consensus        85 ~~~~~~~a~~~~~~~~~~~-~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~-------  155 (256)
                      ..++.++|...+ +..... .-.++.. .+-..+...|++++|...|++..+..  +-+..+|..+-..|...       
T Consensus       225 ~~~~~~~a~~~~-~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~y~~~~~~~~~~  301 (472)
T 4g1t_A          225 EGEEEGEGEKLV-EEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI--PNNAYLHCQIGCCYRAKVFQVMNL  301 (472)
T ss_dssp             -----CHHHHHH-HHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhHHHHHHHHH-HHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC--CChHHHHHHHHHHHHHHHHHhhhH
Confidence            345566676433 333322 2222222 47778889999999999999998875  45667777766555432       


Q ss_pred             ------------CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChh--HHHHHHH-
Q 025225          156 ------------GKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEEL--PFRILLK-  220 (256)
Q Consensus       156 ------------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~--t~~~li~-  220 (256)
                                  +..++|...|++..+.. +.+...|..+-..|.+.|++++|.+.|++..+....|...  .+..+.. 
T Consensus       302 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~  380 (472)
T 4g1t_A          302 RENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNF  380 (472)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Confidence                        33677888888776632 2345778889999999999999999999988775444322  1222222 


Q ss_pred             HhcCCCChHHHHH
Q 025225          221 GLLPHPLLRSKVK  233 (256)
Q Consensus       221 ~~~~~g~~~~a~~  233 (256)
                      .+.+.|+.++|+.
T Consensus       381 ~~~~~~~~~~Ai~  393 (472)
T 4g1t_A          381 QLYQMKCEDKAIH  393 (472)
T ss_dssp             HHHTSSCHHHHHH
T ss_pred             HHHHCCCHHHHHH
Confidence            2346788888887

>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=97.26  E-value=0.0019  Score=44.93  Aligned_cols=103  Identities=12%  Similarity=0.065  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC--CCCC----hhHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP--DPPE----ELPF  215 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g--~~p~----~~t~  215 (256)
                      .++..+=..|.+.|++++|.+.|++..+.  .| +...|+.+-..|.+.|++++|.+.|++..+..  ..++    ..+|
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            45667778889999999999999998874  35 46788899999999999999999999887541  1222    2356


Q ss_pred             HHHHHHhcCCCChHHHHHhhh--hhcCCCccccc
Q 025225          216 RILLKGLLPHPLLRSKVKKDF--EELFPEKHAYD  247 (256)
Q Consensus       216 ~~li~~~~~~g~~~~a~~~~~--~~~~p~~~~~~  247 (256)
                      ..+-..+...|++++|++...  -...||+.+..
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~~~~~~~~~  120 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSEFRDPELVK  120 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSCCHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhCcCHHHHH
Confidence            677778889999999998333  23456655433

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.25  E-value=0.00041  Score=46.41  Aligned_cols=57  Identities=19%  Similarity=0.182  Sum_probs=35.5

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      +-..+.+.|++++|.+.|++..+..  +.+...|..+-.+|.+.|++++|.+.|++..+
T Consensus        10 ~g~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A           10 QGNSLFKQGLYREAVHCYDQLITAQ--PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            3344555666666666666666554  44566666666666666666666666666655

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.25  E-value=0.00061  Score=48.44  Aligned_cols=122  Identities=11%  Similarity=-0.082  Sum_probs=91.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HhhHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPD----AYIYKDLIIALARTGKMNEAMQVWESMRKED-LFPD----SQTYTE  182 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~  182 (256)
                      +-..+...|++++|...+++..+...-.++    ..++..+-..|...|++++|.+.+++..+.. -.++    ...+..
T Consensus        15 l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   94 (164)
T 3ro3_A           15 LGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYS   94 (164)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHH
Confidence            556677899999999999987654200122    2578888999999999999999999876521 0112    456778


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHhC----CCC-CChhHHHHHHHHhcCCCChHHHHH
Q 025225          183 VIRGFLKDGSPADAMNIYEDMIKS----PDP-PEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       183 li~~~~~~g~~~~a~~~~~~M~~~----g~~-p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +-..|...|++++|.+.+++..+.    +-. .....+..+-..|...|++++|.+
T Consensus        95 l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  150 (164)
T 3ro3_A           95 LGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMH  150 (164)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHH
Confidence            888899999999999999987643    221 224567788888999999999988

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.23  E-value=0.0051  Score=42.33  Aligned_cols=93  Identities=13%  Similarity=0.072  Sum_probs=70.8

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      +...-..+.+.|+.++|+..+-+......-.+... .+=.++...|++++|+..|++..+..  .-+...|..+-..|..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHH
Confidence            34445677899999999865543333222222222 35667788999999999999999886  5578899999999999


Q ss_pred             cCCHHHHHHHHHHHHh
Q 025225          155 TGKMNEAMQVWESMRK  170 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~  170 (256)
                      .|++++|.+.|++..+
T Consensus        98 ~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           98 EHNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            9999999999999876

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.22  E-value=0.0033  Score=50.36  Aligned_cols=134  Identities=9%  Similarity=-0.079  Sum_probs=91.3

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPD--AYIYKDLIIAL  152 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~y~~li~~~  152 (256)
                      .....+...|++++|.+ .++.....+  |+..   .+-..+.+.+++++|+..|+...+..  .|.  ...+..+=.++
T Consensus       107 ayA~~L~~~g~y~eA~~-~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~--d~~~~~~a~~~LG~al  181 (282)
T 4f3v_A          107 GFAACEAAQGNYADAME-ALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP--DKFLAGAAGVAHGVAA  181 (282)
T ss_dssp             HHHHHHHHHTCHHHHHH-HHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS--CHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHH-HHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC--CcccHHHHHHHHHHHH
Confidence            34566788999999974 444443322  4332   34446778999999999998544321  121  23677777888


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIL  218 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~l  218 (256)
                      ...|++++|.+.|++.......|.  .......-.++.+.|+.++|..+|+++...  .|+...+..|
T Consensus       182 ~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~~~~~~aL  247 (282)
T 4f3v_A          182 ANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPEPKVAAAL  247 (282)
T ss_dssp             HHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCCHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHHHHHHH
Confidence            999999999999999875433354  234555666677899999999999999987  3443333333

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.22  E-value=0.023  Score=38.73  Aligned_cols=96  Identities=17%  Similarity=0.080  Sum_probs=70.8

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhccCCC---cHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC---HHHHHHHHHH
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRLLKM---DIV-AVLIELERQEETILAVKIFDIIRKQDWYQPD---AYIYKDLIIA  151 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~~y~~li~~  151 (256)
                      .-..+.+.|+.++|+..+.+......-.+   ... .+-.++.+.|++++|...|+...+..  +-+   ...+..+-.+
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~   85 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHH
Confidence            34566789999999865543333332223   122 46677889999999999999998875  333   6778888899


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHh
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFPDSQ  178 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p~~~  178 (256)
                      |...|++++|.+.|++..+.  .|+..
T Consensus        86 ~~~~g~~~~A~~~~~~~~~~--~p~~~  110 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVATQ--YPGSD  110 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--STTSH
T ss_pred             HHHcCCHHHHHHHHHHHHHH--CCCCh
Confidence            99999999999999998874  25543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.14  E-value=0.0074  Score=40.68  Aligned_cols=80  Identities=13%  Similarity=0.087  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          124 LAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       124 ~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      +|++.|++..+..  ..+...|..+-..|...|++++|.+.|++..+.. ..+...|..+-..|.+.|++++|...|++.
T Consensus         3 ~a~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            3 AITERLEAMLAQG--TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CHHHHHHHHHTTT--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3556666666554  4566777777777777777777777777766532 123556667777777777777777777766


Q ss_pred             HhC
Q 025225          204 IKS  206 (256)
Q Consensus       204 ~~~  206 (256)
                      .+.
T Consensus        80 l~~   82 (115)
T 2kat_A           80 LAA   82 (115)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.13  E-value=0.002  Score=43.95  Aligned_cols=100  Identities=12%  Similarity=0.062  Sum_probs=68.0

Q ss_pred             CCCcHHHHHHHHHHHhhccC-CCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRLL-KMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNE  160 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~~-~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~  160 (256)
                      .|+.++|+..+ +...+.+. .|+..    .+-..+...|++++|...|++..+..  +-+..+|..+-.+|...|++++
T Consensus         3 ~g~~~~A~~~~-~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~   79 (117)
T 3k9i_A            3 LGLEAQAVPYY-EKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF--PNHQALRVFYAMVLYNLGRYEQ   79 (117)
T ss_dssp             ----CCCHHHH-HHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHH
T ss_pred             CCcHHHHHHHH-HHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHcCCHHH
Confidence            46666776433 44444321 13322    37777889999999999999999886  5678899999999999999999


Q ss_pred             HHHHHHHHHhC-CCCCCHhhHHHHHHHHH
Q 025225          161 AMQVWESMRKE-DLFPDSQTYTEVIRGFL  188 (256)
Q Consensus       161 a~~~~~~m~~~-g~~p~~~t~~~li~~~~  188 (256)
                      |.+.|++..+. .-.|+...|...|..|.
T Consensus        80 A~~~~~~al~~~p~~~~~~~~~~ai~~~~  108 (117)
T 3k9i_A           80 GVELLLKIIAETSDDETIQSYKQAILFYA  108 (117)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHTHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHH
Confidence            99999988764 22233444444444443

>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=97.08  E-value=0.0087  Score=54.09  Aligned_cols=174  Identities=16%  Similarity=0.123  Sum_probs=116.0

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhcc---------CCCc-----------H----HHHHHHHHHcCCHHHHHHHHHHH
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRL---------LKMD-----------I----VAVLIELERQEETILAVKIFDII  132 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~---------~~~~-----------~----~~li~~~~~~~~~~~a~~~~~~m  132 (256)
                      ...+...-+.|+.++|- .+++......         -.|+           .    ...++...+.|+++.|..+|+..
T Consensus       382 l~~a~~ee~~~~~e~aR-~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A  460 (679)
T 4e6h_A          382 FSLSEQYELNTKIPEIE-TTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKC  460 (679)
T ss_dssp             HHHHHHHHHTTCHHHHH-HHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHH-HHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            33445556678888876 4445544321         0131           1    13566667789999999999999


Q ss_pred             Hhc-CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-
Q 025225          133 RKQ-DWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-  210 (256)
Q Consensus       133 ~~~-~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-  210 (256)
                      .+. +...+......+.+.-.+ .++.+.|.++|+...+. +.-+...|...+.-....|+.+.|..+|++..+....| 
T Consensus       461 ~~~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~  538 (679)
T 4e6h_A          461 RRLKKLVTPDIYLENAYIEYHI-SKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSH  538 (679)
T ss_dssp             HHTGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTT
T ss_pred             HHhcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHH
Confidence            876 423344444444444222 35699999999988875 33356667888888888999999999999988764322 


Q ss_pred             -ChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCcccccchhHhh
Q 025225          211 -EELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYDPPEEIF  253 (256)
Q Consensus       211 -~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~~li~~y  253 (256)
                       ....|...++--.+.|..+.+.+  .......|+......+++=|
T Consensus       539 ~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          539 LLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVNKLEEFTNKY  584 (679)
T ss_dssp             HHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHh
Confidence             44678888888889998887766  34445567665554455444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.01  E-value=0.022  Score=40.90  Aligned_cols=98  Identities=11%  Similarity=-0.052  Sum_probs=73.6

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhc--------cC-------CCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCC
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLR--------LL-------KMDIV----AVLIELERQEETILAVKIFDIIRKQDW  137 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~--------~~-------~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~  137 (256)
                      ...-..+.+.|++++|+..+.+.....        ..       .|...    .+-.++.+.|++++|+..++...+.. 
T Consensus        15 ~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-   93 (162)
T 3rkv_A           15 RQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE-   93 (162)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-
Confidence            334567788999999986554333320        00       12222    36667888999999999999999886 


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHh
Q 025225          138 YQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQ  178 (256)
Q Consensus       138 ~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  178 (256)
                       +.+...|..+-.+|...|++++|...|++..+.  .|+..
T Consensus        94 -p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~  131 (162)
T 3rkv_A           94 -ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAA  131 (162)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGH
T ss_pred             -CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCH
Confidence             668899999999999999999999999998873  46543

>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=96.94  E-value=0.02  Score=49.07  Aligned_cols=126  Identities=12%  Similarity=-0.034  Sum_probs=92.6

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC---------------cHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCC
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM---------------DIV-AVLIELERQEETILAVKIFDIIRKQDWYQ  139 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~  139 (256)
                      +...-..+.+.|++++|+..+.+......-.+               ... .+-.++.+.|++++|+..|++..+..  .
T Consensus       271 ~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~--p  348 (457)
T 1kt0_A          271 VKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD--S  348 (457)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--T
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--C
Confidence            33445678889999999865544333222211               111 36667789999999999999999886  5


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHH-HHHHHHHh
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAM-NIYEDMIK  205 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~-~~~~~M~~  205 (256)
                      .+...|..+-.+|...|++++|...|++..+.  .| +...+..+-..+.+.|+.+++. ..+.+|..
T Consensus       349 ~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          349 ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68899999999999999999999999998874  35 4567888888888888888765 45566643

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.87  E-value=0.0029  Score=42.08  Aligned_cols=66  Identities=14%  Similarity=0.198  Sum_probs=56.5

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ++...|..+-..+.+.|++++|.+.|++..+.. +.+...|..+-..|.+.|++++|.+.|++..+.
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            356778888899999999999999999988742 225788888999999999999999999998876

>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=96.84  E-value=0.023  Score=41.30  Aligned_cols=106  Identities=16%  Similarity=0.082  Sum_probs=78.9

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCC-----CH-----HHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCC
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQP-----DA-----YIYKDLIIALARTGKMNEAMQVWESMRKE-----DLFPD  176 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p-----~~-----~~y~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~  176 (256)
                      .=+.+.+.|++++|+..|++..+..+-.|     +.     ..|+.+-.++.+.|++++|...+++..+.     .+.||
T Consensus        17 ~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd   96 (159)
T 2hr2_A           17 DAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQD   96 (159)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTST
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCc
Confidence            44566788999999999998876641111     23     38999999999999999999999988873     22675


Q ss_pred             H-hhH----HHHHHHHHHcCChhHHHHHHHHHHh-----CCCCCChhHHHH
Q 025225          177 S-QTY----TEVIRGFLKDGSPADAMNIYEDMIK-----SPDPPEELPFRI  217 (256)
Q Consensus       177 ~-~t~----~~li~~~~~~g~~~~a~~~~~~M~~-----~g~~p~~~t~~~  217 (256)
                      - ..|    ...=.++...|++++|+..|++-.+     .|+.+......-
T Consensus        97 ~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~  147 (159)
T 2hr2_A           97 EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMME  147 (159)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHH
T ss_pred             hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            3 567    7777888899999999999998764     366655444433

>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=96.83  E-value=0.021  Score=47.54  Aligned_cols=118  Identities=11%  Similarity=-0.039  Sum_probs=86.2

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhc-------------cCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCC
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLR-------------LLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWY  138 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~-------------~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~  138 (256)
                      +...-..+.+.|+.++|+..+.+.....             ...|...    .+-.++.+.|++++|++.+++..+..  
T Consensus       226 ~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~--  303 (370)
T 1ihg_A          226 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID--  303 (370)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC--
Confidence            4445567788999999986554333210             0223222    36667788999999999999999875  


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHH
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAM  197 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~  197 (256)
                      .-+...|..+-.+|...|++++|.+.|++..+.  .| +...+..+-..+.+.++.+++.
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a~  361 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDKE  361 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            557889999999999999999999999998874  35 4566666666666666666554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.80  E-value=0.0098  Score=47.62  Aligned_cols=126  Identities=10%  Similarity=-0.036  Sum_probs=94.5

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----hhHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS----QTYTEVIRG  186 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~  186 (256)
                      .+-..+...|++++|.++|+.+...+   |+....-.+-..+.+.+++++|+..|++....   |+.    ..+..+=.+
T Consensus       107 ayA~~L~~~g~y~eA~~~l~~~~~~~---p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~---~d~~~~~~a~~~LG~a  180 (282)
T 4f3v_A          107 GFAACEAAQGNYADAMEALEAAPVAG---SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW---PDKFLAGAAGVAHGVA  180 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHTSSCCTT---CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC---SCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcC---CchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc---CCcccHHHHHHHHHHH
Confidence            46777888999999999999988664   54445555666889999999999999866553   332    356777788


Q ss_pred             HHHcCChhHHHHHHHHHHhCCCCCC--hhHHHHHHHHhcCCCChHHHHHh--hhhhcCCC
Q 025225          187 FLKDGSPADAMNIYEDMIKSPDPPE--ELPFRILLKGLLPHPLLRSKVKK--DFEELFPE  242 (256)
Q Consensus       187 ~~~~g~~~~a~~~~~~M~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~~--~~~~~~p~  242 (256)
                      +.+.|++++|++.|++-......|.  .......-.++.+.|+.++|...  ......|+
T Consensus       181 l~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~  240 (282)
T 4f3v_A          181 AANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE  240 (282)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC
T ss_pred             HHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc
Confidence            9999999999999999886544365  23455666778899999999883  23344555

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.75  E-value=0.023  Score=47.60  Aligned_cols=154  Identities=8%  Similarity=-0.095  Sum_probs=105.3

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCc------------------HHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMD------------------IVAVLIELERQEETILAVKIFDIIRKQDWYQPD  141 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~------------------~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  141 (256)
                      ...+.+.|+.++|++.+.+......-..+                  ...+...|.+.|++++|.+.+....+.-.-.++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            44567889999999766544433221111                  224788899999999999999987653211223


Q ss_pred             HHH----HHHHHHHHHhcCCHHHHHHHHHHHHh----CCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC--CC--
Q 025225          142 AYI----YKDLIIALARTGKMNEAMQVWESMRK----EDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS--PD--  208 (256)
Q Consensus       142 ~~~----y~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~--g~--  208 (256)
                      ..+    .+.+=..+...|+.++|.+++++...    .+..+. ..++..+...|...|++++|..++.+....  +.  
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~  170 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDD  170 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhccc
Confidence            222    22222233345899999999988764    233333 457788999999999999999999987643  22  


Q ss_pred             CC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          209 PP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       209 ~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +| ....|..+.+.|...|++++|..
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~A~~  196 (434)
T 4b4t_Q          171 KPSLVDVHLLESKVYHKLRNLAKSKA  196 (434)
T ss_dssp             STHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhCcHHHHHH
Confidence            22 23467888899999999999887

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.72  E-value=0.028  Score=48.79  Aligned_cols=92  Identities=8%  Similarity=-0.151  Sum_probs=58.3

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhc-----CCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----C-CCCCH-hh
Q 025225          113 LIELERQEETILAVKIFDIIRKQ-----DWYQP-DAYIYKDLIIALARTGKMNEAMQVWESMRKE-----D-LFPDS-QT  179 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~-----~~~~p-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-----g-~~p~~-~t  179 (256)
                      +..+...|++++|+.++++..+.     |.--| ...+++.|...|...|++++|..++++..+-     | -.|++ .+
T Consensus       316 a~~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~  395 (490)
T 3n71_A          316 IDKARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMA  395 (490)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence            34455677777777777665432     11112 2356777777777777777777777766531     2 23333 56


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          180 YTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       180 ~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      ++.|-..|...|++++|..++++-.
T Consensus       396 l~nLa~~~~~~G~~~eA~~~~~~Al  420 (490)
T 3n71_A          396 VMRAGLTNWHAGHIEVGHGMICKAY  420 (490)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            7777777777777777777777654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.69  E-value=0.036  Score=34.97  Aligned_cols=55  Identities=16%  Similarity=0.188  Sum_probs=27.8

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      ..+...|++++|...|++..+..  ..+...|..+-..|.+.|++++|.+.|++..+
T Consensus        17 ~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           17 NAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            33444555555555555554443  33444555555555555555555555555444

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=96.60  E-value=0.043  Score=43.64  Aligned_cols=90  Identities=9%  Similarity=-0.080  Sum_probs=78.1

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~  190 (256)
                      +-..+.+.|++++|...|++..+..  .-+...|..+-..|.+.|++++|.+.+++..+.  .| +...|..+-..|.+.
T Consensus        10 ~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~   85 (281)
T 2c2l_A           10 QGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQLEM   85 (281)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHc
Confidence            5567788999999999999998875  558899999999999999999999999998874  34 567888899999999


Q ss_pred             CChhHHHHHHHHHHh
Q 025225          191 GSPADAMNIYEDMIK  205 (256)
Q Consensus       191 g~~~~a~~~~~~M~~  205 (256)
                      |++++|...|.+..+
T Consensus        86 g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           86 ESYDEAIANLQRAYS  100 (281)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999988664

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.58  E-value=0.027  Score=48.19  Aligned_cols=90  Identities=8%  Similarity=0.069  Sum_probs=47.1

Q ss_pred             HHHHHHHcC---CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc----CCHHHHHHHHHHHHhCCCCCCHhhHHHHH
Q 025225          112 VLIELERQE---ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART----GKMNEAMQVWESMRKEDLFPDSQTYTEVI  184 (256)
Q Consensus       112 li~~~~~~~---~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~----g~~~~a~~~~~~m~~~g~~p~~~t~~~li  184 (256)
                      |-..|.+.|   +.++|++.|....+.|  .++...+..+-..|...    ++.++|.+.|++.. .   -+...+..|=
T Consensus       182 Lg~~~~~~g~~~~~~~A~~~~~~aa~~g--~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~---g~~~a~~~Lg  255 (452)
T 3e4b_A          182 LATVYQKKQQPEQQAELLKQMEAGVSRG--TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-P---GYPASWVSLA  255 (452)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHTT--CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-G---GSTHHHHHHH
T ss_pred             HHHHHHHcCCcccHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-C---CCHHHHHHHH
Confidence            444445556   6666666666666665  44555444444444333    46666666666654 2   2333333333


Q ss_pred             HH-H--HHcCChhHHHHHHHHHHhCC
Q 025225          185 RG-F--LKDGSPADAMNIYEDMIKSP  207 (256)
Q Consensus       185 ~~-~--~~~g~~~~a~~~~~~M~~~g  207 (256)
                      .. |  ...++.++|.++|++-.+.|
T Consensus       256 ~~~~~~~~~~d~~~A~~~~~~Aa~~g  281 (452)
T 3e4b_A          256 QLLYDFPELGDVEQMMKYLDNGRAAD  281 (452)
T ss_dssp             HHHHHSGGGCCHHHHHHHHHHHHHTT
T ss_pred             HHHHhCCCCCCHHHHHHHHHHHHHCC
Confidence            33 2  23556666666666655554

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.55  E-value=0.021  Score=36.16  Aligned_cols=80  Identities=15%  Similarity=0.218  Sum_probs=60.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          141 DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       141 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      +...|..+-..|...|++++|.+.|++..+.. +.+...|..+-..|.+.|++++|...|++..+... -+...+..+-.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCHHHHHHHHH
Confidence            35677888888999999999999999987742 22567888888999999999999999999876521 13444444444


Q ss_pred             Hh
Q 025225          221 GL  222 (256)
Q Consensus       221 ~~  222 (256)
                      .+
T Consensus        86 ~~   87 (91)
T 1na3_A           86 AK   87 (91)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.54  E-value=0.11  Score=36.39  Aligned_cols=112  Identities=9%  Similarity=-0.043  Sum_probs=77.2

Q ss_pred             CCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cCCHHHHH
Q 025225           87 KDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TGKMNEAM  162 (256)
Q Consensus        87 ~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g~~~~a~  162 (256)
                      ++.++|+ .+++...+.|. |+.. +=..|...+.+++|++.|+...+.|    ++..+..|=..|..    .++.++|.
T Consensus         9 ~d~~~A~-~~~~~aa~~g~-~~a~-lg~~y~~g~~~~~A~~~~~~Aa~~g----~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A            9 KDLKKAI-QYYVKACELNE-MFGC-LSLVSNSQINKQKLFQYLSKACELN----SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHH-HHHHHHHHTTC-TTHH-HHHHTCTTSCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             cCHHHHH-HHHHHHHcCCC-Hhhh-HHHHHHcCCCHHHHHHHHHHHHcCC----CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            3456666 34445555553 3333 3334444566777888888887776    66777777777777    78888888


Q ss_pred             HHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCC
Q 025225          163 QVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPD  208 (256)
Q Consensus       163 ~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~  208 (256)
                      +.|++..+.|   +...+..|=..|..    .++.++|.++|++-.+.|.
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            8888887763   56667777777777    7788888888888777764

>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=96.54  E-value=0.013  Score=50.11  Aligned_cols=87  Identities=7%  Similarity=-0.004  Sum_probs=68.0

Q ss_pred             cCCHHHHHHHHHHHHhc-----CCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----C-CCCCH-hhHHHHHH
Q 025225          119 QEETILAVKIFDIIRKQ-----DWYQPD-AYIYKDLIIALARTGKMNEAMQVWESMRKE-----D-LFPDS-QTYTEVIR  185 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~-----~~~~p~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-----g-~~p~~-~t~~~li~  185 (256)
                      .|++++|+.++++..+.     |.--|+ ..+++.|-..|...|++++|+.++++..+-     | -.|++ .+|+.|=.
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~  390 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGR  390 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            46889999999876542     212233 378999999999999999999999987641     2 34544 67999999


Q ss_pred             HHHHcCChhHHHHHHHHHHh
Q 025225          186 GFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       186 ~~~~~g~~~~a~~~~~~M~~  205 (256)
                      .|...|++++|..++++-.+
T Consensus       391 ~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          391 LYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhccCHHHHHHHHHHHHH
Confidence            99999999999999987654

>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=96.52  E-value=0.053  Score=49.03  Aligned_cols=146  Identities=14%  Similarity=0.044  Sum_probs=106.8

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhc-c-CCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLR-L-LKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLI  149 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~-~-~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li  149 (256)
                      .|...+....+.++.+.|.. ++....+. + ..+.+.   +.|. +...++.+.|..+|+...+.  +.-+...|...+
T Consensus       436 vWi~y~~~erR~~~l~~AR~-vf~~A~~~~~~~~~~lyi~~A~lE-~~~~~d~e~Ar~ife~~Lk~--~p~~~~~w~~y~  511 (679)
T 4e6h_A          436 VYCVYMNTMKRIQGLAASRK-IFGKCRRLKKLVTPDIYLENAYIE-YHISKDTKTACKVLELGLKY--FATDGEYINKYL  511 (679)
T ss_dssp             HHHHHHHHHHHHHCHHHHHH-HHHHHHHTGGGSCTHHHHHHHHHH-HTTTSCCHHHHHHHHHHHHH--HTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHH-HHHHHHHhcCCCChHHHHHHHHHH-HHhCCCHHHHHHHHHHHHHH--CCCchHHHHHHH
Confidence            45555665566788888864 44555443 2 223333   1222 12235699999999998877  466788888999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCC--CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCC
Q 025225          150 IALARTGKMNEAMQVWESMRKEDLFP--DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHP  226 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g  226 (256)
                      ......|+.+.|..+|++.....-.+  ....|...+.--.+.|+.+.+..+.++|.+.  .|+......+++-|.-.+
T Consensus       512 ~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~--~P~~~~~~~f~~ry~~~~  588 (679)
T 4e6h_A          512 DFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK--FPEVNKLEEFTNKYKVLD  588 (679)
T ss_dssp             HHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--STTCCHHHHHHHHTCBTT
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCcHHHHHHHHhcCCc
Confidence            99999999999999999988754322  3478999999999999999999999999987  466677777788776554

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.47  E-value=0.016  Score=49.68  Aligned_cols=90  Identities=12%  Similarity=0.020  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc----CChhHHHHHHHHHHhCCCCCChhHHH
Q 025225          144 IYKDLIIALARTG---KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD----GSPADAMNIYEDMIKSPDPPEELPFR  216 (256)
Q Consensus       144 ~y~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~----g~~~~a~~~~~~M~~~g~~p~~~t~~  216 (256)
                      .+..|-..|...|   +.++|.+.|++..+.|- ++...+..|-..|...    ++.++|.++|++.. .|   +...+.
T Consensus       178 a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~  252 (452)
T 3e4b_A          178 CYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWV  252 (452)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHH
T ss_pred             HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHH
Confidence            7777777777788   88888888888777653 4444445555566544    57888888888877 33   344444


Q ss_pred             HHHHH-h--cCCCChHHHHHhhhhh
Q 025225          217 ILLKG-L--LPHPLLRSKVKKDFEE  238 (256)
Q Consensus       217 ~li~~-~--~~~g~~~~a~~~~~~~  238 (256)
                      .|-.. |  ...|+.++|++...+.
T Consensus       253 ~Lg~~~~~~~~~~d~~~A~~~~~~A  277 (452)
T 3e4b_A          253 SLAQLLYDFPELGDVEQMMKYLDNG  277 (452)
T ss_dssp             HHHHHHHHSGGGCCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHH
Confidence            44444 3  4577888888743333

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.46  E-value=0.018  Score=49.97  Aligned_cols=81  Identities=5%  Similarity=-0.114  Sum_probs=56.3

Q ss_pred             HhcCCHHHHHHHHHHHHhC---CCC---CC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----CC-CC-ChhHHHHH
Q 025225          153 ARTGKMNEAMQVWESMRKE---DLF---PD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----PD-PP-EELPFRIL  218 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~---g~~---p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----g~-~p-~~~t~~~l  218 (256)
                      -..|++++|+.++++..+.   -+.   |+ ..+++.|...|...|++++|..++++..+.     |- -| ...+++.|
T Consensus       320 ~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nL  399 (490)
T 3n71_A          320 RSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRA  399 (490)
T ss_dssp             HTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            3557788888888776542   222   32 367888888888888888888888876532     22 12 34567788


Q ss_pred             HHHhcCCCChHHHHH
Q 025225          219 LKGLLPHPLLRSKVK  233 (256)
Q Consensus       219 i~~~~~~g~~~~a~~  233 (256)
                      -..|...|++++|..
T Consensus       400 a~~~~~~G~~~eA~~  414 (490)
T 3n71_A          400 GLTNWHAGHIEVGHG  414 (490)
T ss_dssp             HHHHHHTTCHHHHHH
T ss_pred             HHHHHHCCCHHHHHH
Confidence            888888888888877

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.45  E-value=0.12  Score=43.19  Aligned_cols=157  Identities=6%  Similarity=-0.106  Sum_probs=109.5

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH------HHHHHHH-HcCCHHHHHHHHHHHHh----cCCCCCC-HH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV------AVLIELE-RQEETILAVKIFDIIRK----QDWYQPD-AY  143 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~------~li~~~~-~~~~~~~a~~~~~~m~~----~~~~~p~-~~  143 (256)
                      ...+...|.+.|+++++.+.+.......+-.++..      ..+..+. ..|+.++|..++.....    .+ ..+. ..
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~  136 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREK-RVFLKHS  136 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSS-CCSSHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhC-ccHHHHH
Confidence            44567888999999999865543333223223322      1233332 35789999999887653    33 2333 56


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCC--C-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCC--h
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKE--DLF--P-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPE--E  212 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~--g~~--p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~--~  212 (256)
                      ++..+...|...|++++|..++++....  +..  | ....|..++..|...|++++|..++++....    +..|.  .
T Consensus       137 ~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  216 (434)
T 4b4t_Q          137 LSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVA  216 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHH
T ss_pred             HHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHH
Confidence            7888999999999999999999987653  221  2 2467899999999999999999999887642    22221  3


Q ss_pred             hHHHHHHHHhcCCCChHHHHH
Q 025225          213 LPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       213 ~t~~~li~~~~~~g~~~~a~~  233 (256)
                      ..+..+...+...|++++|..
T Consensus       217 ~~~~~~g~~~~~~~~y~~A~~  237 (434)
T 4b4t_Q          217 ELDLMSGILHCEDKDYKTAFS  237 (434)
T ss_dssp             HHHHHHHHHTTSSSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHH
Confidence            566777788889999999877

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.42  E-value=0.033  Score=47.48  Aligned_cols=94  Identities=14%  Similarity=0.034  Sum_probs=74.4

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC--CCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCCCH-h
Q 025225          112 VLIELERQEETILAVKIFDIIRKQD--WYQP----DAYIYKDLIIALARTGKMNEAMQVWESMRKE------DLFPDS-Q  178 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~--~~~p----~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~~-~  178 (256)
                      .+..+.+.|++++|+.++++..+..  .+.|    ...+++.+...|...|++++|+.++++...-      .-.|++ .
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            4666778899999999999887441  0122    2468999999999999999999999987641      234543 7


Q ss_pred             hHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          179 TYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       179 t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      +++.|-..|...|++++|..++++..+
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            799999999999999999999988654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.37  E-value=0.016  Score=37.72  Aligned_cols=57  Identities=16%  Similarity=0.140  Sum_probs=41.9

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPDAY-IYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      -..+.+.|++++|.+.|++..+..  ..+.. .|..+-.+|...|++++|.+.|++..+.
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE--PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC--SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            345667788888888888877764  44556 7777777788888888888888877763

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.36  E-value=0.033  Score=37.34  Aligned_cols=58  Identities=21%  Similarity=0.107  Sum_probs=51.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      .+-..+...|++++|...|++..+..  ..+...|..+-..|...|++++|...|++..+
T Consensus        24 ~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           24 TLGKTYAEHEQFDAALPHLRAALDFD--PTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            46677889999999999999999886  56788999999999999999999999998876

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.32  E-value=0.032  Score=36.61  Aligned_cols=60  Identities=17%  Similarity=0.267  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHH
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDM  203 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M  203 (256)
                      ...|..+-..|...|++++|.+.|++..+..  | +...|..+-..|.+.|++++|.+.|++.
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~a   67 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD--PDYVGTYYHLGKLYERLDRTDDAIDTYAQG   67 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3344444444444445555544444444321  2 2334444444444445555444444443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.29  E-value=0.02  Score=37.66  Aligned_cols=58  Identities=16%  Similarity=0.200  Sum_probs=51.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      .+-..+.+.|++++|...|++..+..  .-+...|..+-.+|...|++++|.+.|++..+
T Consensus        12 ~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A           12 ALAQEHLKHDNASRALALFEELVETD--PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            46677888999999999999999886  45677899999999999999999999998775

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=96.27  E-value=0.019  Score=41.72  Aligned_cols=99  Identities=12%  Similarity=0.003  Sum_probs=57.7

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHhCCCCCC-HhhHHHHHHH
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK----------MNEAMQVWESMRKEDLFPD-SQTYTEVIRG  186 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~----------~~~a~~~~~~m~~~g~~p~-~~t~~~li~~  186 (256)
                      +.+.+++|.+.++...+..  .-+...|+.+=.++...++          +++|...|++..+.  .|+ ...|..+=.+
T Consensus        14 r~~~feeA~~~~~~Ai~l~--P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~a   89 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNA   89 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHH
Confidence            4445666666666666664  4456666655555555544          34666666666652  343 4556666666


Q ss_pred             HHHc-----------CChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          187 FLKD-----------GSPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       187 ~~~~-----------g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      |...           |++++|.+.|++..+.  .|+...|..-++..
T Consensus        90 y~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~~~  134 (158)
T 1zu2_A           90 YTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMT  134 (158)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            6654           3677777777766654  45555554444433

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.26  E-value=0.026  Score=46.28  Aligned_cols=52  Identities=15%  Similarity=0.111  Sum_probs=24.5

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      +.+.|++++|+..++...+..  ..+...|..+-.+|...|++++|.+.|++..
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al  291 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEE--EKNPKALFRRGKAKAELGQMDSARDDFRKAQ  291 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTT
T ss_pred             HHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334445555555555444443  2344444444444555555555555554443

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.26  E-value=0.1  Score=36.56  Aligned_cols=103  Identities=9%  Similarity=-0.040  Sum_probs=83.0

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHH----cCChh
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLK----DGSPA  194 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~  194 (256)
                      .++.++|++.|.+..+.|  .|+..    |=..|...+.+++|.+.|++..+.|   +...+..|=..|..    .++.+
T Consensus         8 ~~d~~~A~~~~~~aa~~g--~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~   78 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN--EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLR   78 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT--CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHH
T ss_pred             ccCHHHHHHHHHHHHcCC--CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHH
Confidence            357899999999999998  55555    5566667788999999999998864   67788888888888    78999


Q ss_pred             HHHHHHHHHHhCCCCCChhHHHHHHHHhcC----CCChHHHHH
Q 025225          195 DAMNIYEDMIKSPDPPEELPFRILLKGLLP----HPLLRSKVK  233 (256)
Q Consensus       195 ~a~~~~~~M~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~  233 (256)
                      +|.++|++-.+.|   +...+..|-..|..    .++.++|++
T Consensus        79 ~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~  118 (138)
T 1klx_A           79 KAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVK  118 (138)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHH
Confidence            9999999998886   45666666666666    789999888

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=95.98  E-value=0.018  Score=47.22  Aligned_cols=61  Identities=11%  Similarity=0.055  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      .|..+-.+|.+.|++++|...|++..+.  .| +...|..+-.+|...|++++|...|++..+.
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l  293 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTE--EEKNPKALFRRGKAKAELGQMDSARDDFRKAQKY  293 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7888899999999999999999998874  34 6788999999999999999999999998765

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=95.66  E-value=0.32  Score=35.23  Aligned_cols=109  Identities=15%  Similarity=0.048  Sum_probs=74.0

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC-----c-------HH-HHHHHHHHcCCHHHHHHHHHHHHhc----CCC
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM-----D-------IV-AVLIELERQEETILAVKIFDIIRKQ----DWY  138 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~-------~~-~li~~~~~~~~~~~a~~~~~~m~~~----~~~  138 (256)
                      +...-..+.+.|++++|+..+-+.+.-..-.|     +       .. .+=.++.+.|++++|+..++...+.    +.+
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~   93 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL   93 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccC
Confidence            34445667889999999966644333221111     1       22 3666788899999999999988876    112


Q ss_pred             CC-CHHHH----HHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHhhHHHHH
Q 025225          139 QP-DAYIY----KDLIIALARTGKMNEAMQVWESMRK-----EDLFPDSQTYTEVI  184 (256)
Q Consensus       139 ~p-~~~~y----~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~li  184 (256)
                      .| +...|    ...=.++...|++++|...|++..+     .|+.+........|
T Consensus        94 ~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~~~  149 (159)
T 2hr2_A           94 NQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVA  149 (159)
T ss_dssp             TSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHHHH
T ss_pred             CCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHH
Confidence            34 45677    8888899999999999999998865     35555544433333

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=95.62  E-value=0.17  Score=40.98  Aligned_cols=211  Identities=7%  Similarity=-0.007  Sum_probs=133.3

Q ss_pred             cCCchHHHHHHHHHhcCC--C---ccccccccCCCC--CCCCcccCcccccccccccCCCCC-CccccccccchhHHHHH
Q 025225            9 SKIPILASIVLQNLTKNP--S---KNFSFLAFKPKS--PIVDFVAHEPILGLRQYHDGRPRG-SLWRGKKLIGKEALFVI   80 (256)
Q Consensus         9 ~~~~~~A~~l~~~m~~~~--~---~~~ll~a~~~~~--~~~~~~~~~~~~~~~~m~~~~~~~-~~~~~~~~~~~~~~~~i   80 (256)
                      ....+.|+++.+.+..-.  .   |+.--..+...+  .+.+.     +..+..+....+.. ..|..+..+   ...++
T Consensus        46 ~e~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~~~~~ee-----L~~~~~~L~~nPk~y~aW~~R~~i---L~~~~  117 (306)
T 3dra_A           46 EEYSERALHITELGINELASHYTIWIYRFNILKNLPNRNLYDE-----LDWCEEIALDNEKNYQIWNYRQLI---IGQIM  117 (306)
T ss_dssp             TCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTTSCHHHH-----HHHHHHHHHHCTTCCHHHHHHHHH---HHHHH
T ss_pred             CCCCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHcccccHHHH-----HHHHHHHHHHCcccHHHHHHHHHH---HHHHH
Confidence            334457888888764322  2   333222222222  44444     77777766544332 122222210   00001


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH-H---HHHHHHHcCCHH--HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-A---VLIELERQEETI--LAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~---li~~~~~~~~~~--~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ......++.++++ .+++.+.+..  |... +   ---.+.+.|.++  ++++.++.+.+..  .-|-..|+.--..+.+
T Consensus       118 ~~l~~~~~~~~EL-~~~~~~l~~~--pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d--~~N~sAW~~R~~ll~~  192 (306)
T 3dra_A          118 ELNNNDFDPYREF-DILEAMLSSD--PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD--LKNNSAWSHRFFLLFS  192 (306)
T ss_dssp             HHTTTCCCTHHHH-HHHHHHHHHC--TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHS
T ss_pred             HhccccCCHHHHH-HHHHHHHHhC--CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHh
Confidence            2221226788888 4556665533  3222 2   122233456666  9999999999987  6788999988777777


Q ss_pred             cCC------HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChh-HHHHHHHHHHhCC--CCCChhHHHHHHHHhcCC
Q 025225          155 TGK------MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPA-DAMNIYEDMIKSP--DPPEELPFRILLKGLLPH  225 (256)
Q Consensus       155 ~g~------~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~-~a~~~~~~M~~~g--~~p~~~t~~~li~~~~~~  225 (256)
                      .+.      ++++.+.++++..... -|...|+-+-..+.+.|+.. .+.++..+..+.+  -..++..+..+.+.|.+.
T Consensus       193 l~~~~~~~~~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~  271 (306)
T 3dra_A          193 KKHLATDNTIDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQ  271 (306)
T ss_dssp             SGGGCCHHHHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHT
T ss_pred             ccccchhhhHHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHcc
Confidence            776      8999999998887532 37889999888888888754 4667777776543  235778889999999999


Q ss_pred             CChHHHHH
Q 025225          226 PLLRSKVK  233 (256)
Q Consensus       226 g~~~~a~~  233 (256)
                      |+.++|++
T Consensus       272 ~~~~~A~~  279 (306)
T 3dra_A          272 KKYNESRT  279 (306)
T ss_dssp             TCHHHHHH
T ss_pred             CCHHHHHH
Confidence            99999998

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=95.45  E-value=0.057  Score=46.04  Aligned_cols=80  Identities=11%  Similarity=-0.023  Sum_probs=63.9

Q ss_pred             hcCCHHHHHHHHHHHHh---CCCCCC----HhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----CC-CC-ChhHHHHHH
Q 025225          154 RTGKMNEAMQVWESMRK---EDLFPD----SQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----PD-PP-EELPFRILL  219 (256)
Q Consensus       154 ~~g~~~~a~~~~~~m~~---~g~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----g~-~p-~~~t~~~li  219 (256)
                      ..|++++|+.++++..+   .-+.|+    ..+++.|-..|...|++++|..++++..+.     |- -| ...+++.|-
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            35789999999998765   223333    378999999999999999999999987642     32 23 356789999


Q ss_pred             HHhcCCCChHHHHH
Q 025225          220 KGLLPHPLLRSKVK  233 (256)
Q Consensus       220 ~~~~~~g~~~~a~~  233 (256)
                      ..|...|++++|..
T Consensus       390 ~~~~~qg~~~eA~~  403 (433)
T 3qww_A          390 RLYMGLENKAAGEK  403 (433)
T ss_dssp             HHHHHTTCHHHHHH
T ss_pred             HHHHhccCHHHHHH
Confidence            99999999999988

>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=95.32  E-value=0.088  Score=44.80  Aligned_cols=85  Identities=13%  Similarity=0.110  Sum_probs=68.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhC---CCCCC----HhhHHHHHHHHHHcCChhHHHHHHHHHHhC-----CC-CC-ChhH
Q 025225          149 IIALARTGKMNEAMQVWESMRKE---DLFPD----SQTYTEVIRGFLKDGSPADAMNIYEDMIKS-----PD-PP-EELP  214 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~---g~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-----g~-~p-~~~t  214 (256)
                      +..+.+.|++++|++++++..+.   -+.|+    ..+++.|...|...|++++|..++++..+.     |- -| ...+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            55566789999999999998753   23333    468999999999999999999999987642     21 23 4567


Q ss_pred             HHHHHHHhcCCCChHHHHH
Q 025225          215 FRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       215 ~~~li~~~~~~g~~~~a~~  233 (256)
                      ++.|-..|...|++++|..
T Consensus       374 l~nLa~~~~~~g~~~eA~~  392 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMK  392 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHH
Confidence            8899999999999999988

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.05  E-value=0.21  Score=35.81  Aligned_cols=81  Identities=9%  Similarity=0.074  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCC--CHhhHHHHHHHHHHcCChhHHH
Q 025225          123 ILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG---KMNEAMQVWESMRKEDLFP--DSQTYTEVIRGFLKDGSPADAM  197 (256)
Q Consensus       123 ~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~g~~~~a~  197 (256)
                      ..+.+-|.+-.+.|  .++..+--.+-.++++++   +.+++..+|++..+.+ .|  +...+=.|=-+|.+.|++++|.
T Consensus        15 ~~~~~~y~~e~~~~--~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           15 LKFEKKFQSEKAAG--SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHTT--CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHccC--CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHH
Confidence            34444444444444  244444444444555544   3445555555544432 12  1111112222334555555555


Q ss_pred             HHHHHHHhC
Q 025225          198 NIYEDMIKS  206 (256)
Q Consensus       198 ~~~~~M~~~  206 (256)
                      +.++...+.
T Consensus        92 ~y~~~lL~i  100 (152)
T 1pc2_A           92 KYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            555555443

>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=94.56  E-value=0.28  Score=40.68  Aligned_cols=123  Identities=12%  Similarity=0.008  Sum_probs=82.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cC-CHHHHH---HHHHHHHhC-CCCCCHhhHHHHHHHHHHcC
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TG-KMNEAM---QVWESMRKE-DLFPDSQTYTEVIRGFLKDG  191 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g-~~~~a~---~~~~~m~~~-g~~p~~~t~~~li~~~~~~g  191 (256)
                      ++.+|..+|++..+..  +-....|..+--+|.-    .+ .-....   .-++..... .-..+..+|.++--.+...|
T Consensus       214 ~~~~A~~l~e~Al~lD--P~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~~~~~~~a~~~~alal~~l~~g  291 (372)
T 3ly7_A          214 SLNRASELLGEIVQSS--PEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELNNLSIIYQIKAVSALVKG  291 (372)
T ss_dssp             HHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTCGGGTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHhCC
Confidence            4689999999999885  3344555544444431    11 111111   222221111 22457788888877777789


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCCccccc
Q 025225          192 SPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPEKHAYD  247 (256)
Q Consensus       192 ~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~~~~~~  247 (256)
                      ++++|...+++..+.+  |+...|..+=..+.-.|+.++|.+  .....+.|...||.
T Consensus       292 d~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~t~~  347 (372)
T 3ly7_A          292 KTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGANTLY  347 (372)
T ss_dssp             CHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHHHHH
T ss_pred             CHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcChHH
Confidence            9999999999999886  888888777888889999999999  44456677766664

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=94.54  E-value=1.4  Score=35.55  Aligned_cols=154  Identities=11%  Similarity=0.102  Sum_probs=102.3

Q ss_pred             hHHHHHHHhhcCC--CcHHHHHHHHHHHhhccCCCcHH-----HHHHHH-HHc---CCHHHHHHHHHHHHhcCCCCCCHH
Q 025225           75 EALFVILGLKRFK--DDEEKLQKFIKTHVLRLLKMDIV-----AVLIEL-ERQ---EETILAVKIFDIIRKQDWYQPDAY  143 (256)
Q Consensus        75 ~~~~~i~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~-----~li~~~-~~~---~~~~~a~~~~~~m~~~~~~~p~~~  143 (256)
                      .|...=..+...+  +.++++ .+.+......-+--..     -++..+ .+.   +++++++.+++.+.+..  .-|-.
T Consensus        69 aWn~R~~~L~~l~~~~~~eeL-~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~--pkny~  145 (306)
T 3dra_A           69 IWIYRFNILKNLPNRNLYDEL-DWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD--PKNHH  145 (306)
T ss_dssp             HHHHHHHHHHTCTTSCHHHHH-HHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC--TTCHH
T ss_pred             HHHHHHHHHHHcccccHHHHH-HHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC--CCCHH
Confidence            3444333444555  788887 4545554433222111     244222 333   78899999999998886  67888


Q ss_pred             HHHHHHHHHHhcCCHH--HHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCC------hhHHHHHHHHHHhCCCCCChhHH
Q 025225          144 IYKDLIIALARTGKMN--EAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGS------PADAMNIYEDMIKSPDPPEELPF  215 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~--~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~------~~~a~~~~~~M~~~g~~p~~~t~  215 (256)
                      +|+----.+.+.|.++  ++.+.++++.+... -|...|+.--..+.+.|.      ++++++.+.++.... .-|...|
T Consensus       146 aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW  223 (306)
T 3dra_A          146 VWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC-PQNPSTW  223 (306)
T ss_dssp             HHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHH
T ss_pred             HHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC-CCCccHH
Confidence            9988888888888888  89999999987543 367777766666666665      788888888877653 2367777


Q ss_pred             HHHHHHhcCCCChHHHHH
Q 025225          216 RILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       216 ~~li~~~~~~g~~~~a~~  233 (256)
                      +..-..+.+.|+..+.+.
T Consensus       224 ~y~~~ll~~~~~~~~~~~  241 (306)
T 3dra_A          224 NYLLGIHERFDRSITQLE  241 (306)
T ss_dssp             HHHHHHHHHTTCCGGGGH
T ss_pred             HHHHHHHHhcCCChHHHH
Confidence            777777777776444443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=94.42  E-value=0.6  Score=42.44  Aligned_cols=104  Identities=7%  Similarity=-0.059  Sum_probs=60.3

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCCh
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  193 (256)
                      ......|++++|+++.+.       ..+...|..+-..+.+.|+++.|++.|.++..         |..+...|...|+.
T Consensus       660 ~~~l~~~~~~~A~~~~~~-------~~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~  723 (814)
T 3mkq_A          660 ELALKVGQLTLARDLLTD-------ESAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNK  723 (814)
T ss_dssp             HHHHHHTCHHHHHHHHTT-------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCH
T ss_pred             ehhhhcCCHHHHHHHHHh-------hCcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCH
Confidence            334556677777666432       34778999999999999999999999998765         23333444444444


Q ss_pred             hHHHHHHHHHHhCCCCCC-------hhHHHHHHHHhcCCCChHHHHH
Q 025225          194 ADAMNIYEDMIKSPDPPE-------ELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       194 ~~a~~~~~~M~~~g~~p~-------~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +....+-+.....|-.-.       ..-+...++.|.+.+++++|+.
T Consensus       724 ~~~~~~~~~a~~~~~~~~A~~~~~~~g~~~~a~~~~~~~~~~~~A~~  770 (814)
T 3mkq_A          724 EGLVTLAKDAETTGKFNLAFNAYWIAGDIQGAKDLLIKSQRFSEAAF  770 (814)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHcCchHHHHHHHHHcCCHHHHHHHHHHcCChHHHHH
Confidence            443333333332221000       1123445556666666666666

>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=94.26  E-value=0.14  Score=37.01  Aligned_cols=113  Identities=17%  Similarity=0.023  Sum_probs=74.6

Q ss_pred             hcCCCcHHHHHHHHHHHhhccCCCcHHH-HHHHHHHcCC----------HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           84 KRFKDDEEKLQKFIKTHVLRLLKMDIVA-VLIELERQEE----------TILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        84 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~-li~~~~~~~~----------~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      .+.+.+++|+..+........-.++... +=.++...++          +++|+..|++..+..  .-+..+|..+=.+|
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld--P~~~~A~~~LG~ay   90 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID--PKKDEAVWCIGNAY   90 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC--cCcHHHHHHHHHHH
Confidence            3455567776555433333333333332 3334444443          579999999999886  55778999999999


Q ss_pred             HhcC-----------CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          153 ARTG-----------KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       153 ~~~g-----------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ...|           ++++|.+.|++..+  +.|+...|..-+..      .++|-+++-+....
T Consensus        91 ~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~------~~ka~el~~~~~~~  147 (158)
T 1zu2_A           91 TSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEM------TAKAPQLHAEAYKQ  147 (158)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHH------HHTHHHHHHHHHHS
T ss_pred             HHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHH------HHhCHhccCccccc
Confidence            8764           89999999999887  46887777666554      34555555555444

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=94.17  E-value=0.61  Score=29.72  Aligned_cols=57  Identities=25%  Similarity=0.337  Sum_probs=47.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCC-CHh-hHHHHHHHHHHcCChhHHHHHHHHHHhCC
Q 025225          149 IIALARTGKMNEAMQVWESMRKEDLFP-DSQ-TYTEVIRGFLKDGSPADAMNIYEDMIKSP  207 (256)
Q Consensus       149 i~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~-t~~~li~~~~~~g~~~~a~~~~~~M~~~g  207 (256)
                      -..+.+.|++++|.+.|++..+.  .| +.. .|..+-..|.+.|++++|.+.|++..+..
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQT--EPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHH--CSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            45677889999999999998874  35 446 78888889999999999999999988763

>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=93.33  E-value=0.86  Score=36.48  Aligned_cols=94  Identities=15%  Similarity=0.134  Sum_probs=75.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCCC---HHHHHHHHHHHHh-----cCCHHHHHHHHHHHHhCCCCC--CHhhHHHHHHHHHHc
Q 025225          121 ETILAVKIFDIIRKQDWYQPD---AYIYKDLIIALAR-----TGKMNEAMQVWESMRKEDLFP--DSQTYTEVIRGFLKD  190 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~---~~~y~~li~~~~~-----~g~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~  190 (256)
                      .+..|...+++..+..   |+   -..|+.+-..|.+     .|+.++|.+.|++..+.  .|  +..++...-+.+|..
T Consensus       178 ~l~~A~a~lerAleLD---P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~L--nP~~~id~~v~YA~~l~~~  252 (301)
T 3u64_A          178 TVHAAVMMLERACDLW---PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRY--CSAHDPDHHITYADALCIP  252 (301)
T ss_dssp             HHHHHHHHHHHHHHHC---TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHH--CCTTCSHHHHHHHHHTTTT
T ss_pred             hHHHHHHHHHHHHHhC---CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHh--CCCCCchHHHHHHHHHHHh
Confidence            3467777777776664   55   6789999999999     49999999999999883  46  378888888888884


Q ss_pred             -CChhHHHHHHHHHHhCCCC--CChhHHHHHH
Q 025225          191 -GSPADAMNIYEDMIKSPDP--PEELPFRILL  219 (256)
Q Consensus       191 -g~~~~a~~~~~~M~~~g~~--p~~~t~~~li  219 (256)
                       |+.+++.+.+++-.+....  |+....|.+-
T Consensus       253 ~gd~~~a~~~L~kAL~a~p~~~P~~~lan~~~  284 (301)
T 3u64_A          253 LNNRAGFDEALDRALAIDPESVPHNKLLVILS  284 (301)
T ss_dssp             TTCHHHHHHHHHHHHHCCGGGCSSCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCCChhHHHHHH
Confidence             9999999999999988776  7766666554

>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=93.14  E-value=0.59  Score=38.76  Aligned_cols=76  Identities=14%  Similarity=0.138  Sum_probs=63.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHH
Q 025225          139 QPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRIL  218 (256)
Q Consensus       139 ~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~l  218 (256)
                      ..+..+|..+-..+...|++++|...+++....+  |+...|..+=..+.-.|++++|.+.|++-...  .|...||.-.
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~~~  349 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLYWI  349 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHHHH
Confidence            6788899988777778899999999999999965  88777777777788899999999999987766  5677776543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=93.10  E-value=0.63  Score=30.59  Aligned_cols=61  Identities=8%  Similarity=0.002  Sum_probs=40.9

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhcC-----CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          110 VAVLIELERQEETILAVKIFDIIRKQD-----WYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       110 ~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      ..|=..+.+.++++.|...|+...+.-     .-.+....|..+-.+|.+.|++++|...+++..+
T Consensus         9 ~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            9 FELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            345666667777777777777655431     0134566777777777778888888887777765

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=92.92  E-value=0.71  Score=30.43  Aligned_cols=87  Identities=14%  Similarity=0.149  Sum_probs=62.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHH
Q 025225          120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNI  199 (256)
Q Consensus       120 ~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  199 (256)
                      ..-++|..|-+++...+  . ...+--+-+..+.+.|++++|..+.+.+.    .||...|-+|-.+  +.|..+++...
T Consensus        21 H~HqEA~tIAdwL~~~~--~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c----~pdlepw~ALce~--rlGl~s~le~r   91 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKG--E-EEAVQLIRLSSLMNRGDYASALQQGNKLA----YPDLEPWLALCEY--RLGLGSALESR   91 (116)
T ss_dssp             TCHHHHHHHHHHHHHTT--C-HHHHHHHHHHHHHHTTCHHHHHHHHTTSC----CGGGHHHHHHHHH--HHTCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCC--c-HHHHHHHHHHHHHcchhHHHHHHhcCCCC----CchHHHHHHHHHH--hcccHHHHHHH
Confidence            35788888888888776  2 33444444667788899999998888776    4899888877554  67888888888


Q ss_pred             HHHHHhCCCCCChhHHH
Q 025225          200 YEDMIKSPDPPEELPFR  216 (256)
Q Consensus       200 ~~~M~~~g~~p~~~t~~  216 (256)
                      +.+|...| .|....|.
T Consensus        92 L~~la~sg-~p~~q~Fa  107 (116)
T 2p58_C           92 LNRLARSQ-DPRIQTFV  107 (116)
T ss_dssp             HHHHTTCC-CHHHHHHH
T ss_pred             HHHHHhCC-CHHHHHHH
Confidence            88887775 34445544

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.87  E-value=1.7  Score=30.59  Aligned_cols=69  Identities=12%  Similarity=0.090  Sum_probs=51.4

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP  209 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  209 (256)
                      .+..-.+..++.+...|+-|+-.++..++.. +.+|+....-.+-.+|.+.|+..+|.+++.+.-+.|++
T Consensus        89 ~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           89 TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            4555667778888888888888888888543 34567777778888888888888888888888777764

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=92.51  E-value=0.63  Score=38.90  Aligned_cols=54  Identities=7%  Similarity=0.112  Sum_probs=27.1

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMR  169 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~  169 (256)
                      .++...|+.++|......+....  ..+...|-.+|.+|.+.|+..+|.+.|++..
T Consensus       179 ~~~l~~g~~~~a~~~l~~~~~~~--P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r  232 (388)
T 2ff4_A          179 EAEIACGRASAVIAELEALTFEH--PYREPLWTQLITAYYLSDRQSDALGAYRRVK  232 (388)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33444455555555555544443  3444455555555555555555555555443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=92.50  E-value=2.8  Score=36.09  Aligned_cols=121  Identities=11%  Similarity=0.059  Sum_probs=77.4

Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 025225           76 ALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIAL  152 (256)
Q Consensus        76 ~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~  152 (256)
                      |..-+.-..+.++.+.|. .++......+..++..   +.+.... .++.+.|..+|+...+..  .-++..|...++..
T Consensus       289 w~~y~~~~~r~~~~~~AR-~i~~~A~~~~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~~~~yid~e  364 (493)
T 2uy1_A          289 RINHLNYVLKKRGLELFR-KLFIELGNEGVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLLKEEFFLFL  364 (493)
T ss_dssp             HHHHHHHHHHHHCHHHHH-HHHHHHTTSCCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHH-HHHHHhhCCCCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHHHHHHHHHH
Confidence            334444444556677665 4444442222111211   2232222 336889999999887763  33455566777777


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          153 ARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                      .+.|+.+.|..+|+...     .....|...+.-=...|+.+.+..+++++.+
T Consensus       365 ~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          365 LRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            88899999999999873     2567788888877778999888888887763

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=92.48  E-value=0.61  Score=38.98  Aligned_cols=78  Identities=15%  Similarity=0.169  Sum_probs=62.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHh-----CCCCCChhHHHHHH
Q 025225          146 KDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIK-----SPDPPEELPFRILL  219 (256)
Q Consensus       146 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~-----~g~~p~~~t~~~li  219 (256)
                      ..++..+...|+.++|...+..+...  .| +...|-.+|.+|.+.|+..+|.+.|++..+     .|+.|+..+=...-
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~--~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~~  252 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFE--HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNE  252 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            45567777889999999999888763  34 778999999999999999999999998754     49999988766554


Q ss_pred             HHhcCC
Q 025225          220 KGLLPH  225 (256)
Q Consensus       220 ~~~~~~  225 (256)
                      ..+...
T Consensus       253 ~il~~~  258 (388)
T 2ff4_A          253 RILRQQ  258 (388)
T ss_dssp             HHHTTC
T ss_pred             HHHcCC
Confidence            444443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=92.48  E-value=1.1  Score=29.31  Aligned_cols=72  Identities=10%  Similarity=0.032  Sum_probs=55.3

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChh
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKE------DLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEEL  213 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~  213 (256)
                      .+..-+-.+=..+.+.|+++.|...|++..+.      .-.+....+..|-.+|.+.|++++|...+++..+.  .|+..
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l--~P~~~   80 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEHQ   80 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCCCH
Confidence            34455556777788899999999999987653      11245678899999999999999999999998764  55543

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=92.28  E-value=0.66  Score=30.51  Aligned_cols=87  Identities=18%  Similarity=0.119  Sum_probs=63.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHH
Q 025225          120 EETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNI  199 (256)
Q Consensus       120 ~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~  199 (256)
                      ..-++|..|-+++...+  . ...+--+-+..+.+.|++++|..+.+.+.    .||...|-+|-.+  +.|..+++...
T Consensus        20 H~HqEA~tIAdwL~~~~--~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c----~pdlepw~ALce~--rlGl~s~le~r   90 (115)
T 2uwj_G           20 HCHEEALCIAEWLERLG--Q-DEAARLIRISSLANQGRYQEALAFAHGNP----WPALEPWFALCEW--HLGLGAALDRR   90 (115)
T ss_dssp             TCHHHHHHHHHHHHHTT--C-HHHHHHHHHHHHHHTTCHHHHHGGGTTCC----CGGGHHHHHHHHH--HTTCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCC--c-HHHHHHHHHHHHHcchhHHHHHHhcCCCC----CchHHHHHHHHHH--hcccHHHHHHH
Confidence            35788888888888776  2 33444444667788899999988887766    4899888877554  78888888888


Q ss_pred             HHHHHhCCCCCChhHHH
Q 025225          200 YEDMIKSPDPPEELPFR  216 (256)
Q Consensus       200 ~~~M~~~g~~p~~~t~~  216 (256)
                      +.+|...| .|....|.
T Consensus        91 L~~la~sg-~p~~q~Fa  106 (115)
T 2uwj_G           91 LAGLGGSS-DPALADFA  106 (115)
T ss_dssp             HHHHHTCS-SHHHHHHH
T ss_pred             HHHHHhCC-CHHHHHHH
Confidence            88888775 34445544

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.07  E-value=1  Score=31.70  Aligned_cols=62  Identities=23%  Similarity=0.049  Sum_probs=52.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLF  174 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~  174 (256)
                      -.|+.+...|.-++-.++..++...  ..|++...-.+-.+|.+-|+..+|.+++.+..++|++
T Consensus        96 ~ALd~lv~~~KkDqLdki~~~~l~n--~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           96 KALDILVIQGKRDKLEEIGREILKN--NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHC----CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHhccHhHHHHHHHHHhcc--CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            3678888899999999999997555  3789999999999999999999999999999998864

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=91.68  E-value=1.3  Score=31.62  Aligned_cols=62  Identities=10%  Similarity=0.069  Sum_probs=46.4

Q ss_pred             HHHHHHHHcC---CHHHHHHHHHHHHhcCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 025225          111 AVLIELERQE---ETILAVKIFDIIRKQDWYQP--DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD  176 (256)
Q Consensus       111 ~li~~~~~~~---~~~~a~~~~~~m~~~~~~~p--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  176 (256)
                      .+=.++++++   +.+++..++++..+..  .|  ....+=.+--+|.+.|++++|.+.++...+  +.|+
T Consensus        37 ~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~--~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~--ieP~  103 (152)
T 1pc2_A           37 EYAWCLVRSKYNDDIRKGIVLLEELLPKG--SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQ--TEPQ  103 (152)
T ss_dssp             HHHHHHHTCSSHHHHHHHHHHHHHHHHHS--CHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHH--HCTT
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHhcC--CccchHHHHHHHHHHHHHccCHHHHHHHHHHHHh--cCCC
Confidence            3666778887   7779999999998875  34  233333444556999999999999999998  3464

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=90.99  E-value=2.7  Score=36.24  Aligned_cols=111  Identities=14%  Similarity=0.117  Sum_probs=77.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHH--HHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYK--DLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFL  188 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~--~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~  188 (256)
                      .++...+.++++.|..+|+.. +..  ..+...|-  +.+.... .++.+.|.++|+...+.-  |+ ...|...++-..
T Consensus       292 y~~~~~r~~~~~~AR~i~~~A-~~~--~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~~~~yid~e~  365 (493)
T 2uy1_A          292 HLNYVLKKRGLELFRKLFIEL-GNE--GVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLLKEEFFLFLL  365 (493)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHH-TTS--CCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHh-hCC--CCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHHHHHHHHHHH
Confidence            445555678899999999998 433  23444454  3333322 236999999999887742  33 345677788788


Q ss_pred             HcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          189 KDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       189 ~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      +.|+.+.|..+|++..     -+...|...++--...|+.+.+.+
T Consensus       366 ~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~  405 (493)
T 2uy1_A          366 RIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRE  405 (493)
T ss_dssp             HHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHH
Confidence            8999999999999973     256778888876667787766544

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=90.96  E-value=3.6  Score=30.20  Aligned_cols=76  Identities=14%  Similarity=0.258  Sum_probs=36.1

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .|=......|+++-|++.|.....          |..+.-.|.-.|+.++-.++-+.-...|      -+|.-...+.-.
T Consensus        39 ~Lg~~AL~~gn~~lAe~cy~~~~D----------~~~L~~Ly~~tg~~e~L~kla~iA~~~g------~~n~af~~~l~l  102 (177)
T 3mkq_B           39 RLIQEALAQGNASLAEMIYQTQHS----------FDKLSFLYLVTGDVNKLSKMQNIAQTRE------DFGSMLLNTFYN  102 (177)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHTTC----------HHHHHHHHHHHTCHHHHHHHHHHHHHTT------CHHHHHHHHHHH
T ss_pred             HHHHHHHHcCChHHHHHHHHHhCC----------HHHHHHHHHHhCCHHHHHHHHHHHHHCc------cHHHHHHHHHHc
Confidence            455555555555555555554331          3334444444455444443333222221      244445555556


Q ss_pred             CChhHHHHHHHH
Q 025225          191 GSPADAMNIYED  202 (256)
Q Consensus       191 g~~~~a~~~~~~  202 (256)
                      |+++++.++|.+
T Consensus       103 Gdv~~~i~lL~~  114 (177)
T 3mkq_B          103 NSTKERSSIFAE  114 (177)
T ss_dssp             TCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH
Confidence            666666666644

>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=90.27  E-value=2  Score=28.33  Aligned_cols=50  Identities=16%  Similarity=0.218  Sum_probs=30.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      |.=+..+-++.+.... ..|++....+.+.+|-+-+++.-|.++|+..+.+
T Consensus        25 D~~e~rrglN~l~~~D-lVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K   74 (109)
T 1v54_E           25 DAWELRKGMNTLVGYD-LVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   74 (109)
T ss_dssp             CHHHHHHHHHHHTTSS-BCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccc-cCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            3344455555555555 6666666666666666666666666666666543

>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=89.84  E-value=2.6  Score=27.87  Aligned_cols=64  Identities=16%  Similarity=0.194  Sum_probs=52.8

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKG  221 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~  221 (256)
                      +.-+..+-++.+-...+.|+.....+.+++|-+.+++.-|.++|+-.+.. +.+...+|..+++-
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHHH
Confidence            56778888888888899999999999999999999999999999988754 22335678877763

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=89.75  E-value=2.8  Score=26.96  Aligned_cols=65  Identities=12%  Similarity=0.034  Sum_probs=30.6

Q ss_pred             CCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          140 PDAYIYKDLIIALARTGK---MNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      .|+..+..+-.++...++   .++|..+|++..+.  .|+ +.....+=..+.+.|++++|...|+++.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            344444444444443333   45555555555542  232 233333334445555555555555555544

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=89.28  E-value=3.3  Score=28.50  Aligned_cols=83  Identities=10%  Similarity=0.076  Sum_probs=38.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHH---HHHHHHHHHhCCCCC-CH-hhHHHHHHHHHHcCChhH
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNE---AMQVWESMRKEDLFP-DS-QTYTEVIRGFLKDGSPAD  195 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~---a~~~~~~m~~~g~~p-~~-~t~~~li~~~~~~g~~~~  195 (256)
                      .+..+.+-|.+-...|  .|+..+--.+-.+++++...++   +..++++..+.+ .| +. ...=.|--|+.+.|++++
T Consensus        16 ~l~~~~~~y~~e~~~~--~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y~~   92 (126)
T 1nzn_A           16 DLLKFEKKFQSEKAAG--SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEK   92 (126)
T ss_dssp             HHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhccC--CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhHHH
Confidence            3444445555444444  2444444444455555554444   555555555432 12 11 111122234445666666


Q ss_pred             HHHHHHHHHhC
Q 025225          196 AMNIYEDMIKS  206 (256)
Q Consensus       196 a~~~~~~M~~~  206 (256)
                      |.+.++.+.+.
T Consensus        93 A~~~~~~lL~~  103 (126)
T 1nzn_A           93 ALKYVRGLLQT  103 (126)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            66666655544

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=88.79  E-value=3.3  Score=26.57  Aligned_cols=48  Identities=8%  Similarity=0.034  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 025225          122 TILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKE  171 (256)
Q Consensus       122 ~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  171 (256)
                      .++|..++++..+..  .-++.....+=..+...|++++|...|+++.+.
T Consensus        25 ~~~A~~~l~~AL~~d--p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A           25 TDEVSLLLEQALQLE--PYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHC--cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            688888888888776  566777777778888889999999999988875

>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=88.40  E-value=9  Score=31.14  Aligned_cols=119  Identities=11%  Similarity=0.107  Sum_probs=85.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc---------
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK-MNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD---------  190 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~---------  190 (256)
                      ++++++.+++.+.+..  .-|-..|+----.+...|. ++++.+.++++.+... -|...|+..-..+.+.         
T Consensus       125 ~~~~EL~~~~k~l~~d--prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~SAW~~R~~ll~~l~~~~~~~~~  201 (331)
T 3dss_A          125 NWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQ  201 (331)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHHSCCC-----
T ss_pred             cHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHhhhccccccc
Confidence            5899999999999987  7799999998888888888 6999999999998543 3777888766666554         


Q ss_pred             -----CChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCC-----------CChHHHHH--hhhhhcCCCc
Q 025225          191 -----GSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPH-----------PLLRSKVK--KDFEELFPEK  243 (256)
Q Consensus       191 -----g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~-----------g~~~~a~~--~~~~~~~p~~  243 (256)
                           +.++++++.+.+..... +-|...|+-+--.+.+.           +.++++++  ...-.+.||.
T Consensus       202 ~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~  271 (331)
T 3dss_A          202 GRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPEN  271 (331)
T ss_dssp             -CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             cccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhCccc
Confidence                 44778888888777542 23666666443333333           34566666  4445667764

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=87.40  E-value=10  Score=33.26  Aligned_cols=97  Identities=7%  Similarity=0.031  Sum_probs=76.3

Q ss_pred             HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcC-ChhHHHH
Q 025225          122 TILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG--KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDG-SPADAMN  198 (256)
Q Consensus       122 ~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g-~~~~a~~  198 (256)
                      ++++++.++.+.+..  .-+..+|+.---.+.+.|  +++++.+.++++.+... -|...|+.---.+.+.| ..+++.+
T Consensus        89 ~~~eL~~~~~~l~~~--pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d~-~N~~aW~~R~~~l~~l~~~~~~el~  165 (567)
T 1dce_A           89 VKAELGFLESCLRVN--PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELA  165 (567)
T ss_dssp             HHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHcCCChHHHHH
Confidence            899999999999886  678889999888888888  77999999999988542 36788888777777888 7889999


Q ss_pred             HHHHHHhCCCCCChhHHHHHHHHh
Q 025225          199 IYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       199 ~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      .++++.+... -|...|+..-..+
T Consensus       166 ~~~~~I~~~p-~n~saW~~r~~ll  188 (567)
T 1dce_A          166 FTDSLITRNF-SNYSSWHYRSCLL  188 (567)
T ss_dssp             HHHTTTTTTC-CCHHHHHHHHHHH
T ss_pred             HHHHHHHHCC-CCccHHHHHHHHH
Confidence            9998877643 2555666544443

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=87.39  E-value=14  Score=32.33  Aligned_cols=64  Identities=6%  Similarity=0.031  Sum_probs=29.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG-KMNEAMQVWESMRKEDLFPDSQTYTEVIRGF  187 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g-~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  187 (256)
                      +++++++.++.+.+..  .-|-.+|+.---.+.+.| ..+++.+.++++.+... -|...|+..-..+
T Consensus       124 ~~~~el~~~~k~l~~d--~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p-~n~saW~~r~~ll  188 (567)
T 1dce_A          124 NWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLL  188 (567)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhc--cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCC-CCccHHHHHHHHH
Confidence            3455555555555544  344555555444444444 45555555555444321 1344444443333

>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=85.62  E-value=5.5  Score=27.83  Aligned_cols=71  Identities=17%  Similarity=0.264  Sum_probs=44.4

Q ss_pred             HHHHHHcC-CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 025225          113 LIELERQE-ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIR  185 (256)
Q Consensus       113 i~~~~~~~-~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  185 (256)
                      ..-|.+.. |.=+..+-++.+.... ..|++....+.+.+|-+-+++.-|.++|+-.+.+ +.+...+|..++.
T Consensus        59 ~~~F~~~~iD~wElrrglN~l~~~D-lVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~lq  130 (152)
T 2y69_E           59 VTYFNKPDIDAWELRKGMNTLVGYD-LVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ  130 (152)
T ss_dssp             HHHHTCTTCCHHHHHHHHHHHTTSS-BCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             HHHcCCcCccHHHHHHHHHHHhccc-cCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHHH
Confidence            33344444 5556666666666666 6777777777777777777777777777776653 1223444555544

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=85.09  E-value=8.6  Score=34.73  Aligned_cols=103  Identities=9%  Similarity=0.025  Sum_probs=64.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .+=..+.+.++++.|++.|..+..          |..+...|...|+.+...++-+.....|      -++.-...|.+.
T Consensus       686 ~la~~al~~~~~~~A~~~y~~~~d----------~~~l~~l~~~~~~~~~~~~~~~~a~~~~------~~~~A~~~~~~~  749 (814)
T 3mkq_A          686 ALGDASLQRFNFKLAIEAFTNAHD----------LESLFLLHSSFNNKEGLVTLAKDAETTG------KFNLAFNAYWIA  749 (814)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHTC----------HHHHHHHHHHTTCHHHHHHHHHHHHHTT------CHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHccC----------hhhhHHHHHHcCCHHHHHHHHHHHHHcC------chHHHHHHHHHc
Confidence            577788889999999999998762          4455666666777776666655555433      235555556667


Q ss_pred             CChhHHHHHHHHHHh--------CCCCCCh----hHHHHHHHHhcCCCChH
Q 025225          191 GSPADAMNIYEDMIK--------SPDPPEE----LPFRILLKGLLPHPLLR  229 (256)
Q Consensus       191 g~~~~a~~~~~~M~~--------~g~~p~~----~t~~~li~~~~~~g~~~  229 (256)
                      |++++|.+++.++.+        ....|..    ......-..+...|+.+
T Consensus       750 g~~~~a~~~~~~~~~~~~A~~lA~~~~~~~~~i~~~~~~~~~~L~~~~~~~  800 (814)
T 3mkq_A          750 GDIQGAKDLLIKSQRFSEAAFLGSTYGLGDNEVNDIVTKWKENLILNGKNT  800 (814)
T ss_dssp             TCHHHHHHHHHHTTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             CCHHHHHHHHHHcCChHHHHHHHHHhCCChHHHHHHHHHHHHHHHhccchh
Confidence            777777777766543        1234455    34444445555666643

>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=84.14  E-value=8.7  Score=26.86  Aligned_cols=45  Identities=20%  Similarity=0.219  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHH
Q 025225          160 EAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMI  204 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~  204 (256)
                      +..+-++.+....+.|+.....+.+++|-+.+++.-|.++|+-.+
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK  115 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVK  115 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            334444444444445555555555555555555555555554444

>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=83.86  E-value=9.7  Score=30.42  Aligned_cols=95  Identities=9%  Similarity=0.010  Sum_probs=67.6

Q ss_pred             CCHHHHHHHHH-HHHhc--C------CHHHHHHHHHHHHhCCCCCC---HhhHHHHHHHHHHc-----CChhHHHHHHHH
Q 025225          140 PDAYIYKDLII-ALART--G------KMNEAMQVWESMRKEDLFPD---SQTYTEVIRGFLKD-----GSPADAMNIYED  202 (256)
Q Consensus       140 p~~~~y~~li~-~~~~~--g------~~~~a~~~~~~m~~~g~~p~---~~t~~~li~~~~~~-----g~~~~a~~~~~~  202 (256)
                      +....|...+. ++...  |      ...+|..++++..+  +.|+   -..|+.|-..|.+.     |+.++|.+.|++
T Consensus       152 ve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAle--LDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~fer  229 (301)
T 3u64_A          152 VGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACD--LWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEH  229 (301)
T ss_dssp             HHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHH--HCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHH--hCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHH
Confidence            44455665554 44443  2      25666666776666  4577   56899999999994     999999999999


Q ss_pred             HHhCCCCCChhHHHHHHHHhcCC-CChHHHHHhhh
Q 025225          203 MIKSPDPPEELPFRILLKGLLPH-PLLRSKVKKDF  236 (256)
Q Consensus       203 M~~~g~~p~~~t~~~li~~~~~~-g~~~~a~~~~~  236 (256)
                      -.+.+-.-+..++...-+.++.. |+.+++.+...
T Consensus       230 AL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~  264 (301)
T 3u64_A          230 LTRYCSAHDPDHHITYADALCIPLNNRAGFDEALD  264 (301)
T ss_dssp             HHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHH
T ss_pred             HHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            98764322467788888999985 88888777333

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=83.67  E-value=3.4  Score=32.53  Aligned_cols=116  Identities=10%  Similarity=-0.032  Sum_probs=62.1

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHHHhcCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDW-YQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~-~~p~~~~y~~li~~~~~~g~  157 (256)
                      +..+.+.|.+.+++..+....+...-..+.. .++.-+|-.|+++.|.+-++...+... ..|...+|-.+|.+      
T Consensus         4 ~~~ll~~g~L~~al~~~~~~VR~~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~a------   77 (273)
T 1zbp_A            4 WKNALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKA------   77 (273)
T ss_dssp             HHHHTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH------
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHH------
Confidence            3455677777777766665555544433444 477777888888887777776665530 12222334333332      


Q ss_pred             HHHHHHHHHHHHhCCCCCC-----HhhHHHHHHHHHH--cCChhHHHHHHHHHHh
Q 025225          158 MNEAMQVWESMRKEDLFPD-----SQTYTEVIRGFLK--DGSPADAMNIYEDMIK  205 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g~~p~-----~~t~~~li~~~~~--~g~~~~a~~~~~~M~~  205 (256)
                          +..=++.-..+-.|.     ..-...|+.+...  .|+.++|.++-....+
T Consensus        78 ----E~~R~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e  128 (273)
T 1zbp_A           78 ----AQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEE  128 (273)
T ss_dssp             ----HHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ----HHHHHHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Confidence                222222222222222     2234455555553  4777777777766643

>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=83.57  E-value=17  Score=29.76  Aligned_cols=85  Identities=7%  Similarity=0.085  Sum_probs=57.7

Q ss_pred             cC-CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhc-C-CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChh-
Q 025225          119 QE-ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALART-G-KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPA-  194 (256)
Q Consensus       119 ~~-~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~-g-~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~-  194 (256)
                      .| +++++++.++.+.+..  .-+..+|+.--..+.+. + +++++.++++++.+.. .-|...|+.---.+.+.|..+ 
T Consensus       101 l~~~l~eEL~~~~~~L~~n--PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~  177 (349)
T 3q7a_A          101 LNKSLEDELRLMNEFAVQN--LKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGR  177 (349)
T ss_dssp             TTCCHHHHHHHHHHHHHTT--CCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTC
T ss_pred             hhhhHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccc
Confidence            45 5888888888888775  56777788777777766 6 7788888888877642 125666665544444445454 


Q ss_pred             -------HHHHHHHHHHhC
Q 025225          195 -------DAMNIYEDMIKS  206 (256)
Q Consensus       195 -------~a~~~~~~M~~~  206 (256)
                             +++++++++.+.
T Consensus       178 ~~~~~~~eELe~~~k~I~~  196 (349)
T 3q7a_A          178 ISEAQWGSELDWCNEMLRV  196 (349)
T ss_dssp             CCHHHHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHHHHHHHHh
Confidence                   677777777665

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=81.23  E-value=10  Score=26.02  Aligned_cols=62  Identities=10%  Similarity=0.029  Sum_probs=44.4

Q ss_pred             HHHHHHHHcCCHHH---HHHHHHHHHhcCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 025225          111 AVLIELERQEETIL---AVKIFDIIRKQDWYQP--DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD  176 (256)
Q Consensus       111 ~li~~~~~~~~~~~---a~~~~~~m~~~~~~~p--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  176 (256)
                      .+-.++.++.+...   ++.++.++.+.+  .|  .....=.|--++.+.|++++|.+.++.+.+.  .|+
T Consensus        40 ~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~--~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~~~lL~~--eP~  106 (126)
T 1nzn_A           40 EYAWCLVRTRYNDDIRKGIVLLEELLPKG--SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQ  106 (126)
T ss_dssp             HHHHHHTTSSSHHHHHHHHHHHHHHTTTS--CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHhcC--CcchHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh--CCC
Confidence            36667777776555   999999988775  34  2223334456788999999999999999883  464

---

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	256
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.9
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.85
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.7
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.32
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.2
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.17
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.16
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.09
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.06
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.02
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.96
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.89
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.83
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.83
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.8
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.76
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.7
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.65
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.6
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.58
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.51
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.45
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.4
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.28
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.27
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.25
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.21
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.15
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.98
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.78
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.73
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.57
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.53
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.51
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.34
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.34
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.29
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.11
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	95.94
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.79
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	95.79
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.53
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.36
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.0
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	94.95
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	94.91
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.17
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	92.64
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	92.47
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	91.44
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	89.69
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	87.73
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	87.7
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	87.14
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	84.76
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	83.99
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	81.27
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	80.52

>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=98.90  E-value=8.7e-08  Score=77.28  Aligned_cols=173  Identities=13%  Similarity=0.081  Sum_probs=122.3

Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           77 LFVILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        77 ~~~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      ..+...+...|+.++|+..+. ...... ..+... .+-..+.+.|++++|...|++..+..  +-+..+|..+-..|..
T Consensus       207 ~~l~~~~~~~~~~~~A~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~  283 (388)
T d1w3ba_         207 INLGNVLKEARIFDRAVAAYL-RALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANALKE  283 (388)
T ss_dssp             HHHHHHHHTTTCTTHHHHHHH-HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHHHHH
T ss_pred             HHHhhhhhccccHHHHHHHHH-HhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHH
Confidence            334456667777777775443 333322 222222 36667778889999999998887775  4567788888888899


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHHhcCCCChHHHHH
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .|++++|.+.|+..... .+.+...+..+...|.+.|++++|.+.|++..+.  .| +...|..+-..|.+.|++++|.+
T Consensus       284 ~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~  360 (388)
T d1w3ba_         284 KGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALM  360 (388)
T ss_dssp             HSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHH
T ss_pred             cCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            99999999988877653 2346678888888888999999999999987764  34 45667888889999999999988


Q ss_pred             hhh--hhcCCC-cccccchhHhhcc
Q 025225          234 KDF--EELFPE-KHAYDPPEEIFGK  255 (256)
Q Consensus       234 ~~~--~~~~p~-~~~~~~li~~y~~  255 (256)
                      ...  -.+.|+ ...|..|..+|.+
T Consensus       361 ~~~~al~l~P~~~~a~~~lg~~~~~  385 (388)
T d1w3ba_         361 HYKEAIRISPTFADAYSNMGNTLKE  385 (388)
T ss_dssp             HHHHHHTTCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            333  344565 3456666666643

>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=98.85  E-value=6e-08  Score=78.27  Aligned_cols=202  Identities=11%  Similarity=0.030  Sum_probs=147.2

Q ss_pred             ccccCCchHHHHHHHHHhcCC--C---ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNP--S---KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~--~---~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +...+..+.|.+.++...+..  .   |..+-..+...++.+.+     +..+.......+..         ...+..+-
T Consensus       179 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~~~~~~~~~---------~~~~~~l~  244 (388)
T d1w3ba_         179 FNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRA-----VAAYLRALSLSPNH---------AVVHGNLA  244 (388)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHH-----HHHHHHHHHHCTTC---------HHHHHHHH
T ss_pred             ccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHH-----HHHHHHhHHHhhhH---------HHHHHHHH
Confidence            345677888888887754322  1   44455566667777776     77776655433222         23344456


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN  159 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~  159 (256)
                      ..+.+.|+.++|+..+-+......-.++.. .+-..+...|++++|.+.++...+..  +.+...+..+...|.+.|+++
T Consensus       245 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~  322 (388)
T d1w3ba_         245 CVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC--PTHADSLNNLANIKREQGNIE  322 (388)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC--CccchhhhHHHHHHHHCCCHH
Confidence            677889999999865533332222212222 47788899999999999999998885  788899999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCC-hhHHHHHHHHhcCCCC
Q 025225          160 EAMQVWESMRKEDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPE-ELPFRILLKGLLPHPL  227 (256)
Q Consensus       160 ~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~-~~t~~~li~~~~~~g~  227 (256)
                      +|.+.|++..+.  .|+ ...|..+-..|.+.|++++|.+.|++..+.  .|+ ...|..+-..|.+.|+
T Consensus       323 ~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         323 EAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCC
Confidence            999999998763  464 567888999999999999999999998765  454 5577888777766653

>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=98.70  E-value=6.2e-08  Score=77.21  Aligned_cols=209  Identities=10%  Similarity=0.042  Sum_probs=153.2

Q ss_pred             ccccCCchHHHHHHHHHhcCCC-----ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHH
Q 025225            6 FSRSKIPILASIVLQNLTKNPS-----KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVI   80 (256)
Q Consensus         6 ~~~~~~~~~A~~l~~~m~~~~~-----~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i   80 (256)
                      +-+.|+.+.|.+.|+...+...     |..+-..+...++...+     +..|.+.....+..         ...+..+.
T Consensus        29 ~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A-----~~~~~~al~~~p~~---------~~~~~~la   94 (323)
T d1fcha_          29 RLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLA-----ISALRRCLELKPDN---------QTALMALA   94 (323)
T ss_dssp             HHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHHHCTTC---------HHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHH-----HHHHHhhhcccccc---------cccccccc
Confidence            4467899999999999765433     55555666777777777     88887665433221         23445556


Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhcc-CCCcH-----H-----------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRL-LKMDI-----V-----------AVLIELERQEETILAVKIFDIIRKQDWYQPDAY  143 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~-----~-----------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  143 (256)
                      ..|...|+.++|++.+ +...... -.+..     .           ..+..+...+...+|.+.|.+..+..+-.++..
T Consensus        95 ~~~~~~~~~~~A~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~  173 (323)
T d1fcha_          95 VSFTNESLQRQACEIL-RDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPD  173 (323)
T ss_dssp             HHHHHTTCHHHHHHHH-HHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHH
T ss_pred             ccccccccccccccch-hhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccc
Confidence            7788999999998554 3433211 00000     0           133445566778889999988776653456788


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHHHHH
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRILLKG  221 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~li~~  221 (256)
                      ++..+-..+...|++++|...|++....  .| +...|..+-..|.+.|++++|.+.|++..+.  .| +...|..+-..
T Consensus       174 ~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~  249 (323)
T d1fcha_         174 VQCGLGVLFNLSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGIS  249 (323)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             cchhhHHHHHHHHHHhhhhccccccccc--ccccccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHH
Confidence            8999999999999999999999998764  24 4678889999999999999999999998765  33 45678889999


Q ss_pred             hcCCCChHHHHH
Q 025225          222 LLPHPLLRSKVK  233 (256)
Q Consensus       222 ~~~~g~~~~a~~  233 (256)
                      |.+.|++++|++
T Consensus       250 ~~~~g~~~~A~~  261 (323)
T d1fcha_         250 CINLGAHREAVE  261 (323)
T ss_dssp             HHHHTCHHHHHH
T ss_pred             HHHCCCHHHHHH
Confidence            999999999988

>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=98.32  E-value=4.8e-05  Score=59.82  Aligned_cols=159  Identities=14%  Similarity=0.059  Sum_probs=112.5

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK  157 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~  157 (256)
                      -..+.+.|+.++|+..+ +...+.. -.++.. .+-.++...|++++|...|++..+..  +-+...|..+...|...|+
T Consensus        26 g~~~~~~g~~~~A~~~~-~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          26 GLRRLQEGDLPNAVLLF-EAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK--PDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHTTCHHHHHHHH-HHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHH-HHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc--ccccccccccccccccccc
Confidence            44567889999998544 4444332 112222 36677888899999999999888775  4567888888889999999


Q ss_pred             HHHHHHHHHHHHhCC-----------------------------------------------C---CCCHhhHHHHHHHH
Q 025225          158 MNEAMQVWESMRKED-----------------------------------------------L---FPDSQTYTEVIRGF  187 (256)
Q Consensus       158 ~~~a~~~~~~m~~~g-----------------------------------------------~---~p~~~t~~~li~~~  187 (256)
                      +++|.+.+++.....                                               .   .++...+..+-..+
T Consensus       103 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~  182 (323)
T d1fcha_         103 QRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLF  182 (323)
T ss_dssp             HHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHH
T ss_pred             ccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHH
Confidence            999988888765321                                               0   12344566667778


Q ss_pred             HHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHHhh--hhhcCCC
Q 025225          188 LKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVKKD--FEELFPE  242 (256)
Q Consensus       188 ~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~--~~~~~p~  242 (256)
                      ...|++++|...|++..+... -+...|..+-..|.+.|++++|++..  .-.+.|+
T Consensus       183 ~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~  238 (323)
T d1fcha_         183 NLSGEYDKAVDCFTAALSVRP-NDYLLWNKLGATLANGNQSEEAVAAYRRALELQPG  238 (323)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHhhhhccccccccccc-ccccchhhhhhcccccccchhHHHHHHHHHHHhhc
Confidence            889999999999998776521 24667888888999999999998832  2334554

>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=98.20  E-value=0.00011  Score=57.74  Aligned_cols=167  Identities=14%  Similarity=-0.007  Sum_probs=119.4

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCC-cHH--HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKM-DIV--AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      -|........+.|+.+++.. +++......... ...  ..+..+.+.|+.+.|.++|+...+.+  ..+...|-.....
T Consensus       101 l~~~ya~~~~~~~~~~~a~~-i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~--~~~~~~~~~~a~~  177 (308)
T d2onda1         101 LYFAYADYEESRMKYEKVHS-IYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA--RTRHHVYVTAALM  177 (308)
T ss_dssp             HHHHHHHHHHHTTCHHHHHH-HHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST--TCCTHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccHHHHHH-HHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC--CCcHHHHHHHHHH
Confidence            34444556678899999874 555555433222 212  57888889999999999999999886  3444445444333


Q ss_pred             -HHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC-CCCCC--hhHHHHHHHHhcCCCC
Q 025225          152 -LARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS-PDPPE--ELPFRILLKGLLPHPL  227 (256)
Q Consensus       152 -~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-g~~p~--~~t~~~li~~~~~~g~  227 (256)
                       +...|+.+.|..+|+.+.+. ...+...|...+..+.+.|++++|..+|++-.+. +..|.  ...|...+.--..+|+
T Consensus       178 e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~  256 (308)
T d2onda1         178 EYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGD  256 (308)
T ss_dssp             HHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSC
T ss_pred             HHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCC
Confidence             34568999999999999875 2335788999999999999999999999998765 45554  4578888888788899


Q ss_pred             hHHHHHh--hhhhcCCCccc
Q 025225          228 LRSKVKK--DFEELFPEKHA  245 (256)
Q Consensus       228 ~~~a~~~--~~~~~~p~~~~  245 (256)
                      .+.+.+.  -.....|+..+
T Consensus       257 ~~~~~~~~~r~~~~~~~~~~  276 (308)
T d2onda1         257 LASILKVEKRRFTAFREEYE  276 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTTTS
T ss_pred             HHHHHHHHHHHHHHCccccc
Confidence            8888772  22344555433

>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=98.17  E-value=5.9e-05  Score=50.50  Aligned_cols=97  Identities=13%  Similarity=0.056  Sum_probs=79.5

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCCh
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSP  193 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  193 (256)
                      +.+.+.|++++|+..|++..+..  +-+...|..+-.+|.+.|++++|.+.+++..+.+ +.+...|..+-..|...|++
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC--CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCH
Confidence            45677899999999999988885  6788889999999999999999999999888743 24678888888999999999


Q ss_pred             hHHHHHHHHHHhCCCCCChhHH
Q 025225          194 ADAMNIYEDMIKSPDPPEELPF  215 (256)
Q Consensus       194 ~~a~~~~~~M~~~g~~p~~~t~  215 (256)
                      ++|...|++-.+.  .|+...+
T Consensus        88 ~~A~~~~~~a~~~--~p~~~~~  107 (117)
T d1elwa_          88 EEAKRTYEEGLKH--EANNPQL  107 (117)
T ss_dssp             HHHHHHHHHHHTT--CTTCHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHH
Confidence            9999999988865  4554443

>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=98.16  E-value=1.8e-05  Score=62.45  Aligned_cols=195  Identities=10%  Similarity=-0.018  Sum_probs=131.5

Q ss_pred             chHHHHHHHHHhcCCC------ccccccccCCCCCCCCcccCcccccccccccCCCCCCccccccccchhHHHHHHHhhc
Q 025225           12 PILASIVLQNLTKNPS------KNFSFLAFKPKSPIVDFVAHEPILGLRQYHDGRPRGSLWRGKKLIGKEALFVILGLKR   85 (256)
Q Consensus        12 ~~~A~~l~~~m~~~~~------~~~ll~a~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~i~~~~~   85 (256)
                      .+.|.++++...+...      |........+.+..+.+     ..+|+.+....+..        ....|...+....+
T Consensus        80 ~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a-----~~i~~~~l~~~~~~--------~~~~w~~~~~~~~~  146 (308)
T d2onda1          80 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKV-----HSIYNRLLAIEDID--------PTLVYIQYMKFARR  146 (308)
T ss_dssp             HHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHTSSSSC--------THHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHH-----HHHHHHHHHHhcCC--------hHHHHHHHHHHHHH
Confidence            4567777777544211      33333334455556666     77887776543322        12345566777778


Q ss_pred             CCCcHHHHHHHHHHHhhcc-CCCcHHH--HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 025225           86 FKDDEEKLQKFIKTHVLRL-LKMDIVA--VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAM  162 (256)
Q Consensus        86 ~~~~~~a~~~~~~~~~~~~-~~~~~~~--li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~  162 (256)
                      .++.+.+.. +++...+.. ..+....  ..-.+...|+.+.|..+|+...+..  ..+...|...+..+.+.|+++.|.
T Consensus       147 ~~~~~~ar~-i~~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~--p~~~~~w~~y~~~~~~~g~~~~aR  223 (308)
T d2onda1         147 AEGIKSGRM-IFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTR  223 (308)
T ss_dssp             HHCHHHHHH-HHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHH
T ss_pred             cCChHHHHH-HHHHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh--hhhHHHHHHHHHHHHHcCChHHHH
Confidence            888999875 445554433 2222221  1122334689999999999999874  677899999999999999999999


Q ss_pred             HHHHHHHhC-CCCCC--HhhHHHHHHHHHHcCChhHHHHHHHHHHhC-CCCCChhHHHHHHHHh
Q 025225          163 QVWESMRKE-DLFPD--SQTYTEVIRGFLKDGSPADAMNIYEDMIKS-PDPPEELPFRILLKGL  222 (256)
Q Consensus       163 ~~~~~m~~~-g~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~M~~~-g~~p~~~t~~~li~~~  222 (256)
                      .+|++..+. ...|+  ...|...+.--.+.|+.+.+..+++++.+. .-.+.......++.-|
T Consensus       224 ~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~ry  287 (308)
T d2onda1         224 VLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREEYEGKETALLVDRY  287 (308)
T ss_dssp             HHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTTSSCHHHHHHTTT
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCccccccchHHHHHHHH
Confidence            999998775 34554  468999999888999999999999998764 3334444555555444

>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=98.09  E-value=1.9e-05  Score=53.63  Aligned_cols=105  Identities=15%  Similarity=0.120  Sum_probs=83.8

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCCCH-hhHHHHHHH
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGK---MNEAMQVWESMRKEDLFPDS-QTYTEVIRG  186 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~-~t~~~li~~  186 (256)
                      .+++.+...+++++|++.|+...+.+  +.++.++..+-.++.+.++   +++|.++|++....+-.|+. .+|..|=.+
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~--p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAG--SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            57888999999999999999999887  7788899999888887654   45699999998875433432 367778888


Q ss_pred             HHHcCChhHHHHHHHHHHhCCCCCChhHHHHHH
Q 025225          187 FLKDGSPADAMNIYEDMIKSPDPPEELPFRILL  219 (256)
Q Consensus       187 ~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li  219 (256)
                      |.+.|++++|.+.|++..+.  .|+......+.
T Consensus        82 y~~~g~~~~A~~~~~~aL~~--~P~~~~A~~l~  112 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQT--EPQNNQAKELE  112 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHHh--CcCCHHHHHHH
Confidence            99999999999999999885  46655444333

>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=98.06  E-value=7.6e-05  Score=52.74  Aligned_cols=89  Identities=17%  Similarity=0.127  Sum_probs=78.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCC
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGS  192 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~  192 (256)
                      +.|.+.|++++|...|++..+..  +-+...|..+-.+|...|++++|.+.|++..+..  | +...|..+...|...|+
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~--p~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--KKYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHhhhccccc--hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc--ccchHHHHHHHHHHHHcCC
Confidence            45778999999999999999886  6788999999999999999999999999988742  5 45789999999999999


Q ss_pred             hhHHHHHHHHHHhC
Q 025225          193 PADAMNIYEDMIKS  206 (256)
Q Consensus       193 ~~~a~~~~~~M~~~  206 (256)
                      +++|.+.|++..+.
T Consensus        94 ~~eA~~~~~~a~~~  107 (159)
T d1a17a_          94 FRAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc
Confidence            99999999998876

>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=98.02  E-value=5.6e-05  Score=55.17  Aligned_cols=87  Identities=10%  Similarity=-0.035  Sum_probs=58.0

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCC
Q 025225          114 IELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGS  192 (256)
Q Consensus       114 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~  192 (256)
                      +.+.+.|++++|+..|++..+..  +-++..|+.+-.+|.+.|++++|...|++..+  +.| +...|..+-.+|.+.|+
T Consensus        12 n~~~~~g~~~~Ai~~~~kal~~~--p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~lg~~~~~l~~   87 (201)
T d2c2la1          12 NRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFFLGQCQLEMES   87 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHHHHHHHHHCCC
Confidence            45666777777777777666664  45666677777777777777777777776654  334 35566667777777777


Q ss_pred             hhHHHHHHHHHH
Q 025225          193 PADAMNIYEDMI  204 (256)
Q Consensus       193 ~~~a~~~~~~M~  204 (256)
                      +++|...|++..
T Consensus        88 ~~~A~~~~~~al   99 (201)
T d2c2la1          88 YDEAIANLQRAY   99 (201)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            777777776654

>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=97.96  E-value=8.8e-05  Score=49.20  Aligned_cols=92  Identities=11%  Similarity=0.091  Sum_probs=72.9

Q ss_pred             cHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHH
Q 025225          108 DIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRG  186 (256)
Q Consensus       108 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~  186 (256)
                      +...+-..+.+.|++++|...|++..+..  +-++..|..+-.+|.+.|++++|+..|++..+.  .| +...|..+-..
T Consensus        18 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~a~~~la~~   93 (112)
T d1hxia_          18 NPMEEGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVS   93 (112)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhccccccccc--ccccccchHHHHHH
Confidence            33445556777888999999999888775  447888888888888999999999999887773  34 46778888888


Q ss_pred             HHHcCChhHHHHHHHHH
Q 025225          187 FLKDGSPADAMNIYEDM  203 (256)
Q Consensus       187 ~~~~g~~~~a~~~~~~M  203 (256)
                      |...|+.++|.+.|++.
T Consensus        94 y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          94 HTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHH
Confidence            88889999998888764

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.89  E-value=0.0011  Score=49.76  Aligned_cols=119  Identities=15%  Similarity=0.005  Sum_probs=80.8

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      .+-..|.+.|+.++|+..|-+.+....-.|... .+=.++.+.|++++|...|++..+..  +-+..+|..+-..|...|
T Consensus        42 ~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g  119 (259)
T d1xnfa_          42 ERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAHLNRGIALYYGG  119 (259)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH--hhhhhhHHHHHHHHHHHh
Confidence            344677889999999866654443322222222 36677889999999999999999886  456778888889999999


Q ss_pred             CHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIY  200 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~  200 (256)
                      ++++|.+.|++..+..  | +......+..++.+.+..+.+..+.
T Consensus       120 ~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (259)
T d1xnfa_         120 RDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLK  162 (259)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhc--cccHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            9999999999887642  3 3333333333444444444333333

>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=97.83  E-value=0.00014  Score=52.62  Aligned_cols=75  Identities=15%  Similarity=0.160  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHH-----hCCCCCChhHHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMI-----KSPDPPEELPFR  216 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~-----~~g~~p~~~t~~  216 (256)
                      ..+..+...+.+.|++++|...+++..+.  .| +...|..++.+|.+.|+.++|.+.|++..     +.|+.|+..|-.
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~--~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~~  145 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFE--HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  145 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHHH
Confidence            46777888888999999999999988873  34 67889999999999999999999998874     358999877644


Q ss_pred             HHH
Q 025225          217 ILL  219 (256)
Q Consensus       217 ~li  219 (256)
                      ..-
T Consensus       146 l~~  148 (179)
T d2ff4a2         146 LNE  148 (179)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=0.00045  Score=50.33  Aligned_cols=128  Identities=13%  Similarity=-0.042  Sum_probs=92.5

Q ss_pred             HhhcCCCcHHHHHHHHHHHhhccCCCcHH---HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           82 GLKRFKDDEEKLQKFIKTHVLRLLKMDIV---AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        82 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      .+...|++++|++.+ ...    ..|+..   .+=.++.+.|++++|++.|++..+..  +-+...|..+=.+|.+.|++
T Consensus        14 ~~~~~~d~~~Al~~~-~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld--p~~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          14 LAADKKDWKGALDAF-SAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD--KHLAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHTTCHHHHHHHH-HTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHCCCHHHHHHHH-Hhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh--hhhhhhHHHHHHHHHhhccH
Confidence            456788899998554 322    234433   36667788999999999999998886  67888999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCC---------------HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHH
Q 025225          159 NEAMQVWESMRKEDLFPD---------------SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFR  216 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~---------------~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~  216 (256)
                      ++|.+-|++.....-..+               ..++..+-..|.+.|++++|.+.|.+..+....|......
T Consensus        87 ~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~~~~~  159 (192)
T d1hh8a_          87 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKID  159 (192)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHHH
T ss_pred             HHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcchHHHH
Confidence            999999998765311100               1334556667888999999999998877775555444443

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.80  E-value=0.00093  Score=50.28  Aligned_cols=91  Identities=13%  Similarity=0.053  Sum_probs=79.9

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHHc
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD-SQTYTEVIRGFLKD  190 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~  190 (256)
                      +=..|.+.|++++|.+.|++..+..  +-++.+|+.+-.+|.+.|++++|.+.|++..+.  .|+ ...|..+-..|...
T Consensus        43 ~G~~y~~~g~~~~A~~~~~~al~l~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~  118 (259)
T d1xnfa_          43 RGVLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYG  118 (259)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHHhhccC--CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH--HhhhhhhHHHHHHHHHHH
Confidence            4457788999999999999999886  668899999999999999999999999999884  354 56788888899999


Q ss_pred             CChhHHHHHHHHHHhC
Q 025225          191 GSPADAMNIYEDMIKS  206 (256)
Q Consensus       191 g~~~~a~~~~~~M~~~  206 (256)
                      |++++|.+.|++..+.
T Consensus       119 g~~~~A~~~~~~al~~  134 (259)
T d1xnfa_         119 GRDKLAQDDLLAFYQD  134 (259)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhh
Confidence            9999999999998765

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.76  E-value=0.0026  Score=46.09  Aligned_cols=114  Identities=9%  Similarity=-0.048  Sum_probs=90.8

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChh
Q 025225          115 ELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPA  194 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~  194 (256)
                      .+...|++++|++.|.++     ..|++.+|..+=..|...|++++|.+.|++..+.. +-+...|..+=..|.+.|+++
T Consensus        14 ~~~~~~d~~~Al~~~~~i-----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~   87 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYD   87 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHCCCHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHH
Confidence            346789999999999864     26788899999999999999999999999988743 125678888989999999999


Q ss_pred             HHHHHHHHHHhC------------CCCC--C-hhHHHHHHHHhcCCCChHHHHHh
Q 025225          195 DAMNIYEDMIKS------------PDPP--E-ELPFRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       195 ~a~~~~~~M~~~------------g~~p--~-~~t~~~li~~~~~~g~~~~a~~~  234 (256)
                      +|.+.|++-.+.            |...  + ..++..+-.+|.+.|++++|.+.
T Consensus        88 ~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~  142 (192)
T d1hh8a_          88 LAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQ  142 (192)
T ss_dssp             HHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHH
Confidence            999999987642            1111  1 24455667788999999999983

>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=97.70  E-value=0.00085  Score=44.53  Aligned_cols=96  Identities=11%  Similarity=-0.054  Sum_probs=75.0

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      -+.+.+.|+.++|+..+.+......-.+... .+=.++.+.|++++|+..++...+..  +.++..|..+-.+|...|++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK--PDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhc--cchhhHHHHHHHHHHHccCH
Confidence            3456789999999965544443333323322 36667788999999999999999987  77999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHhh
Q 025225          159 NEAMQVWESMRKEDLFPDSQT  179 (256)
Q Consensus       159 ~~a~~~~~~m~~~g~~p~~~t  179 (256)
                      ++|...|++..+.  .|+...
T Consensus        88 ~~A~~~~~~a~~~--~p~~~~  106 (117)
T d1elwa_          88 EEAKRTYEEGLKH--EANNPQ  106 (117)
T ss_dssp             HHHHHHHHHHHTT--CTTCHH
T ss_pred             HHHHHHHHHHHHh--CCCCHH
Confidence            9999999998873  466443

>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=97.65  E-value=0.00018  Score=48.90  Aligned_cols=93  Identities=14%  Similarity=0.225  Sum_probs=75.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCC----HhhHHHHHH
Q 025225          112 VLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKED--LFPD----SQTYTEVIR  185 (256)
Q Consensus       112 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~----~~t~~~li~  185 (256)
                      +=+.+.+.|++++|++.|++..+.+  +.+...|..+-.+|.+.|++++|.+.+++..+..  ....    ..+|..+-.
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~   87 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELD--PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGN   87 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence            3456888999999999999999886  6789999999999999999999999999987621  1111    246667777


Q ss_pred             HHHHcCChhHHHHHHHHHHhC
Q 025225          186 GFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       186 ~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      .+...+++++|.+.|++-...
T Consensus        88 ~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          88 SYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHhc
Confidence            788889999999999876654

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=0.00047  Score=54.34  Aligned_cols=82  Identities=2%  Similarity=0.039  Sum_probs=43.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHH
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNI  199 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~  199 (256)
                      ++++|+..++...+..  +-+..+|+.+-..+.+.|++++|.+.|+++.+.  .| +...|+.+...+.+.|++++|.+.
T Consensus        93 ~~~eal~~~~~al~~~--p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~  168 (315)
T d2h6fa1          93 DLHEEMNYITAIIEEQ--PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQY  168 (315)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHH
T ss_pred             CHHHHHHHHHHHHHHH--HhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHH
Confidence            3555555555555443  344555555555555555555555555555542  12 345555555555555555555555


Q ss_pred             HHHHHhC
Q 025225          200 YEDMIKS  206 (256)
Q Consensus       200 ~~~M~~~  206 (256)
                      |++..+.
T Consensus       169 ~~~al~~  175 (315)
T d2h6fa1         169 VDQLLKE  175 (315)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555443

>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=97.58  E-value=0.0013  Score=46.05  Aligned_cols=90  Identities=16%  Similarity=0.013  Sum_probs=71.0

Q ss_pred             HHHhhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCH
Q 025225           80 ILGLKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKM  158 (256)
Q Consensus        80 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~  158 (256)
                      =+.|.+.|++++|+..|-+......-.+... .+-.+|...|++++|.+.|+...+..  +-+..+|..+..+|...|++
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~--p~~~~a~~~~g~~~~~~g~~   94 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--KKYIKGYYRRAASNMALGKF   94 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc--ccchHHHHHHHHHHHHcCCH
Confidence            3467899999999966544333222112222 36778889999999999999999886  66889999999999999999


Q ss_pred             HHHHHHHHHHHhC
Q 025225          159 NEAMQVWESMRKE  171 (256)
Q Consensus       159 ~~a~~~~~~m~~~  171 (256)
                      ++|.+.|++..+.
T Consensus        95 ~eA~~~~~~a~~~  107 (159)
T d1a17a_          95 RAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9999999999884

>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=97.51  E-value=0.00072  Score=48.87  Aligned_cols=91  Identities=16%  Similarity=0.050  Sum_probs=77.6

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCC-ChhHHHHH
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPP-EELPFRIL  218 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p-~~~t~~~l  218 (256)
                      |+...+...=..|.+.|++++|...|++..+.. +-+...|+.+-.+|.+.|++++|...|++..+.  .| +...|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            666677777788999999999999999887742 236678999999999999999999999998765  45 46678899


Q ss_pred             HHHhcCCCChHHHHH
Q 025225          219 LKGLLPHPLLRSKVK  233 (256)
Q Consensus       219 i~~~~~~g~~~~a~~  233 (256)
                      -.+|.+.|++++|+.
T Consensus        79 g~~~~~l~~~~~A~~   93 (201)
T d2c2la1          79 GQCQLEMESYDEAIA   93 (201)
T ss_dssp             HHHHHHTTCHHHHHH
T ss_pred             HHHHHHCCCHHHHHH
Confidence            999999999999988

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.45  E-value=0.0025  Score=45.14  Aligned_cols=62  Identities=6%  Similarity=-0.014  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      .+|+.+-.+|.+.|++++|+..+++..+.  .| ++..|..+-.+|...|++++|...|++..+.
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~--~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALEL--DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhc--cccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            34555566666667777777666666653  24 5566666666666667777777777666553

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.40  E-value=0.006  Score=47.68  Aligned_cols=168  Identities=15%  Similarity=0.138  Sum_probs=113.5

Q ss_pred             HHHHHHhhcCC-CcHHHHHHHHHHHhhccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 025225           77 LFVILGLKRFK-DDEEKLQKFIKTHVLRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIA  151 (256)
Q Consensus        77 ~~~i~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~  151 (256)
                      ...-..+...+ +.++|+. +++...+.  .|+..    .+-..+.+.|++++|++.++.+.+..  +-+...|+.+-..
T Consensus        81 ~~r~~~l~~l~~~~~eal~-~~~~al~~--~p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~d--p~n~~a~~~~~~~  155 (315)
T d2h6fa1          81 HFRRVLLKSLQKDLHEEMN-YITAIIEE--QPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWV  155 (315)
T ss_dssp             HHHHHHHHHTTCCHHHHHH-HHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcCHHHHHH-HHHHHHHH--HHhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhh--hcchHHHHHHHHH
Confidence            33333444544 3677763 33343322  23322    24555678899999999999999886  6789999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHHcCC------hhHHHHHHHHHHhCCCCCChhHHHHHHHHhcC
Q 025225          152 LARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLKDGS------PADAMNIYEDMIKSPDPPEELPFRILLKGLLP  224 (256)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~------~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~  224 (256)
                      +.+.|++++|.+.|++..+.+  | +...|+.+-..+.+.+.      +++|.+.+.+..+.. +-+...|+.+-..|..
T Consensus       156 ~~~~~~~~~Al~~~~~al~~~--p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~  232 (315)
T d2h6fa1         156 IQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD  232 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT
T ss_pred             HHHHHhhHHHHHHHHHHHHHC--CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh
Confidence            999999999999999999843  4 56778877666666665      467888888776653 2367778877766665


Q ss_pred             CCChHHHHH--hhhhhcCCCc---ccccchhHhh
Q 025225          225 HPLLRSKVK--KDFEELFPEK---HAYDPPEEIF  253 (256)
Q Consensus       225 ~g~~~~a~~--~~~~~~~p~~---~~~~~li~~y  253 (256)
                      .| .+++.+  .....+.|+.   ..+..++++|
T Consensus       233 ~~-~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y  265 (315)
T d2h6fa1         233 RG-LSKYPNLLNQLLDLQPSHSSPYLIAFLVDIY  265 (315)
T ss_dssp             TC-GGGCHHHHHHHHHHTTTCCCHHHHHHHHHHH
T ss_pred             cC-hHHHHHHHHHHHHhCCCcCCHHHHHHHHHHH
Confidence            55 577666  2234455553   3344555554

>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=97.28  E-value=0.007  Score=46.53  Aligned_cols=157  Identities=13%  Similarity=-0.002  Sum_probs=103.9

Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHh---hccCCCcHH----HHHHHHHHcCCHHHHHHHHHHHHhc----CCCCCCHHHHH
Q 025225           78 FVILGLKRFKDDEEKLQKFIKTHV---LRLLKMDIV----AVLIELERQEETILAVKIFDIIRKQ----DWYQPDAYIYK  146 (256)
Q Consensus        78 ~~i~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~----~li~~~~~~~~~~~a~~~~~~m~~~----~~~~p~~~~y~  146 (256)
                      ..-..|...+++++|++.+.+...   +.+-.++..    .+-.+|.+.|++++|.+.++...+.    |.......++.
T Consensus        42 ~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~  121 (290)
T d1qqea_          42 QAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKF  121 (290)
T ss_dssp             HHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHH
Confidence            345677889999999866644432   222333332    3667788999999999999976543    21122245566


Q ss_pred             HHHHHHHh-cCCHHHHHHHHHHHHh----CCCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC-----CCh-hH
Q 025225          147 DLIIALAR-TGKMNEAMQVWESMRK----EDLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP-----PEE-LP  214 (256)
Q Consensus       147 ~li~~~~~-~g~~~~a~~~~~~m~~----~g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~-----p~~-~t  214 (256)
                      .+...|-. .|++++|.+.|++..+    .+-.+. ..+|..+...|.+.|++++|.+.|++.......     ++. ..
T Consensus       122 ~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~  201 (290)
T d1qqea_         122 ELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDY  201 (290)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHH
T ss_pred             HHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHH
Confidence            66666644 6999999999998754    122221 356888899999999999999999998765221     111 11


Q ss_pred             HHHHHHHhcCCCChHHHHHh
Q 025225          215 FRILLKGLLPHPLLRSKVKK  234 (256)
Q Consensus       215 ~~~li~~~~~~g~~~~a~~~  234 (256)
                      |...+-.+...|++..|.+.
T Consensus       202 ~~~~~~~~l~~~d~~~A~~~  221 (290)
T d1qqea_         202 FLKKGLCQLAATDAVAAART  221 (290)
T ss_dssp             HHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHH
Confidence            23344466677888888773

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.27  E-value=0.0062  Score=42.15  Aligned_cols=91  Identities=10%  Similarity=-0.054  Sum_probs=60.1

Q ss_pred             HHHHcCCHHHHHHHHHHHHhcCC---CCC-----------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhH
Q 025225          115 ELERQEETILAVKIFDIIRKQDW---YQP-----------DAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTY  180 (256)
Q Consensus       115 ~~~~~~~~~~a~~~~~~m~~~~~---~~p-----------~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  180 (256)
                      .+.+.|++.+|+..|.+..+.-.   ..+           ...+|+.+-.+|.+.|++++|.+.+++..+.. +.++..|
T Consensus        26 ~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~  104 (153)
T d2fbna1          26 EFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKAL  104 (153)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhh
Confidence            44455666666666665443210   011           12466677777788888888888888777642 2266788


Q ss_pred             HHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          181 TEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       181 ~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ..+-.+|...|++++|...|++-.+.
T Consensus       105 ~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1         105 YKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            88888888888888888888877665

>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=97.25  E-value=0.00046  Score=46.42  Aligned_cols=98  Identities=10%  Similarity=0.088  Sum_probs=75.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCC---hhHHHHHHHHHHhCCCCCCh-hHHHHHHHH
Q 025225          146 KDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGS---PADAMNIYEDMIKSPDPPEE-LPFRILLKG  221 (256)
Q Consensus       146 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~---~~~a~~~~~~M~~~g~~p~~-~t~~~li~~  221 (256)
                      ..+++.+...+++++|++.|++....+ +.+..++..+-.++.+.++   +++|.++|++..+....|+. ..|..+-.+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            467888999999999999999988743 2356777888888877554   45799999998887655553 367788899


Q ss_pred             hcCCCChHHHHH--hhhhhcCCCcc
Q 025225          222 LLPHPLLRSKVK--KDFEELFPEKH  244 (256)
Q Consensus       222 ~~~~g~~~~a~~--~~~~~~~p~~~  244 (256)
                      |.+.|++++|.+  ...-.+.|+-.
T Consensus        82 y~~~g~~~~A~~~~~~aL~~~P~~~  106 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQTEPQNN  106 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHhhhHHHHHHHHHHHHhCcCCH
Confidence            999999999999  33344567644

>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=97.21  E-value=0.003  Score=41.32  Aligned_cols=88  Identities=14%  Similarity=0.117  Sum_probs=68.6

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 025225           79 VILGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG  156 (256)
Q Consensus        79 ~i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g  156 (256)
                      .-..+-+.|+.++|+..+ +...... -.+... .+-.++.+.|++++|+..|+...+..  +-+...|..+-..|...|
T Consensus        22 ~g~~~~~~g~~~~A~~~~-~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~la~~y~~~g   98 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAF-EAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEH   98 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHH-HHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHH-hhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccc--cccccchHHHHHHHHHCC
Confidence            345677899999998555 4444332 222222 36667888999999999999999886  667999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 025225          157 KMNEAMQVWESMR  169 (256)
Q Consensus       157 ~~~~a~~~~~~m~  169 (256)
                      ++++|.+.|++..
T Consensus        99 ~~~~A~~~l~~~l  111 (112)
T d1hxia_          99 NANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHh
Confidence            9999999998753

>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=97.15  E-value=0.018  Score=44.10  Aligned_cols=159  Identities=9%  Similarity=-0.007  Sum_probs=100.6

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHh---hccCCCcHH----HHHHHHHH-cCCHHHHHHHHHHHHhc----CCCCC-C
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHV---LRLLKMDIV----AVLIELER-QEETILAVKIFDIIRKQ----DWYQP-D  141 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~----~li~~~~~-~~~~~~a~~~~~~m~~~----~~~~p-~  141 (256)
                      .+..+-..|.+.|++++|+..+.+...   ..+......    .+...|-. .|++++|.+.|++..+.    + -.+ -
T Consensus        79 ~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~-~~~~~  157 (290)
T d1qqea_          79 TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQ-SVALS  157 (290)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT-CHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcC-chhhh
Confidence            444556778899999999855543222   122111111    24444534 69999999999976532    2 111 2


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH------hhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC-CC---
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS------QTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP-PE---  211 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~------~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~-p~---  211 (256)
                      ..+|..+...|...|++++|.+.|++..........      ..|..++-.+...|+++.|...|++..+.... |+   
T Consensus       158 ~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre  237 (290)
T d1qqea_         158 NKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRE  237 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------
T ss_pred             hhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHH
Confidence            456788899999999999999999998774221111      11334445666789999999999998876321 22   


Q ss_pred             hhHHHHHHHHhcCC--CChHHHHHh
Q 025225          212 ELPFRILLKGLLPH--PLLRSKVKK  234 (256)
Q Consensus       212 ~~t~~~li~~~~~~--g~~~~a~~~  234 (256)
                      ......++.++-..  +.+++|++.
T Consensus       238 ~~~l~~l~~a~~~~d~e~~~eai~~  262 (290)
T d1qqea_         238 SNFLKSLIDAVNEGDSEQLSEHCKE  262 (290)
T ss_dssp             HHHHHHHHHHHHTTCTTTHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            23456677777653  457788773

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.98  E-value=0.0021  Score=46.09  Aligned_cols=67  Identities=9%  Similarity=0.101  Sum_probs=60.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHhh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK-----EDLFPDSQT  179 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t  179 (256)
                      .+...+.+.|++++|...++...+..  .-+...|..++.+|.+.|+.++|.+.|+++.+     .|+.|...+
T Consensus        72 ~la~~~~~~g~~~~Al~~~~~al~~~--P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          72 AKAEAEIACGRASAVIAELEALTFEH--PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHCCCchHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            37778889999999999999999986  78999999999999999999999999999854     489998654

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.78  E-value=0.00094  Score=51.25  Aligned_cols=51  Identities=18%  Similarity=0.122  Sum_probs=33.4

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      +.|++++|+..+++..+..  +-|...+..+...|+..|++++|.+.|+...+
T Consensus         8 ~~G~l~eAl~~l~~al~~~--P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~   58 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIK   58 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4466666666666666664  55666666666666666666666666666655

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.73  E-value=0.023  Score=39.20  Aligned_cols=93  Identities=17%  Similarity=0.069  Sum_probs=69.1

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCC----------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCCH
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPD----------AYIYKDLIIALARTGKMNEAMQVWESMRKE-----DLFPDS  177 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~----------~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~~  177 (256)
                      -....+.|++++|++.|++..+...-.|+          ..+|+.+-.+|.+.|++++|.+-+++..+.     ...++.
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~   95 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDE   95 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccc
Confidence            34456779999999999987754312232          468899999999999999999999987642     222322


Q ss_pred             -----hhHHHHHHHHHHcCChhHHHHHHHHHHh
Q 025225          178 -----QTYTEVIRGFLKDGSPADAMNIYEDMIK  205 (256)
Q Consensus       178 -----~t~~~li~~~~~~g~~~~a~~~~~~M~~  205 (256)
                           ..|+.+=.+|.+.|++++|.+.|++..+
T Consensus        96 ~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          96 GKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                 2466677889999999999999998653

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.57  E-value=0.0021  Score=49.15  Aligned_cols=122  Identities=6%  Similarity=-0.181  Sum_probs=74.6

Q ss_pred             hhcCCCcHHHHHHHHHHHhhccCCCcHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 025225           83 LKRFKDDEEKLQKFIKTHVLRLLKMDIV-AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEA  161 (256)
Q Consensus        83 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a  161 (256)
                      ..+.|+.++|+..+.+..+...-.++.. .+...++..|++++|.+.|+...+..  .-+...+..+-..+...+..+++
T Consensus         6 aL~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~--P~~~~~~~~l~~ll~a~~~~~~a   83 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLF--PEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHhccccHHH
Confidence            3577999999976654444333333333 59999999999999999999998875  33445554444444333333222


Q ss_pred             HHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          162 MQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       162 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ..-...-...+-.++...+......+.+.|+.++|.+.+.+..+.
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            111111001111122344444556677889999999999998764

>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=96.53  E-value=0.045  Score=38.28  Aligned_cols=93  Identities=8%  Similarity=-0.039  Sum_probs=69.6

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccC----CCcHH------------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLL----KMDIV------------AVLIELERQEETILAVKIFDIIRKQDWYQPDAYI  144 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~------------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~  144 (256)
                      +.+.+.|++++|+..|-+......-    .....            .+-.+|.+.|++++|+..++...+..  +-++.+
T Consensus        21 ~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~--p~~~~a   98 (170)
T d1p5qa1          21 TVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD--SNNEKG   98 (170)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc--ccchhh
Confidence            3567889999998655433322111    11100            14455778999999999999999886  568999


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 025225          145 YKDLIIALARTGKMNEAMQVWESMRKEDLFPDS  177 (256)
Q Consensus       145 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  177 (256)
                      |..+-.+|...|++++|...|++..+.  .|+-
T Consensus        99 ~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n  129 (170)
T d1p5qa1          99 LSRRGEAHLAVNDFELARADFQKVLQL--YPNN  129 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSC
T ss_pred             hHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCC
Confidence            999999999999999999999999873  4643

>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=96.51  E-value=0.046  Score=38.07  Aligned_cols=52  Identities=15%  Similarity=-0.031  Sum_probs=25.5

Q ss_pred             HHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          117 ERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       117 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      .+.|++++|+..++...+..  +.+...|..+-.+|...|++++|.+.|++..+
T Consensus        75 ~~l~~~~~Ai~~~~~al~l~--p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~  126 (168)
T d1kt1a1          75 LKLREYTKAVECCDKALGLD--SANEKGLYRRGEAQLLMNEFESAKGDFEKVLE  126 (168)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhhhcccchhhhhhhhhcc--cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34455555555555444443  34444444445555555555555555555444

>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=96.34  E-value=0.048  Score=37.37  Aligned_cols=95  Identities=13%  Similarity=0.062  Sum_probs=70.9

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhccCCC---cHH--------------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRLLKM---DIV--------------AVLIELERQEETILAVKIFDIIRKQDWYQPDAY  143 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~--------------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  143 (256)
                      +.+.+.|++.+|+..+-+.+......+   +..              .+-.+|.+.|++++|++.++...+..  +.++.
T Consensus        25 ~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~--p~~~k  102 (153)
T d2fbna1          25 NEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID--KNNVK  102 (153)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc--chhhh
Confidence            567789999999865543332111111   110              14555678999999999999999886  67899


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhh
Q 025225          144 IYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQT  179 (256)
Q Consensus       144 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  179 (256)
                      +|-.+-.+|...|++++|...|++..+.  .|+-..
T Consensus       103 a~~~~g~~~~~lg~~~~A~~~~~~al~l--~P~n~~  136 (153)
T d2fbna1         103 ALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLD  136 (153)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHH
T ss_pred             hhHHhHHHHHHcCCHHHHHHHHHHHHHh--CCCCHH
Confidence            9999999999999999999999998873  465433

>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=96.34  E-value=0.0067  Score=40.60  Aligned_cols=90  Identities=9%  Similarity=0.116  Sum_probs=69.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCC---CC--CC-hhHHHHHH
Q 025225          146 KDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSP---DP--PE-ELPFRILL  219 (256)
Q Consensus       146 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g---~~--p~-~~t~~~li  219 (256)
                      ..+=..|.+.|++++|.+.|.+..+.+ +.+...|..+-..|.+.|++++|.+.+++..+..   ..  ++ ..+|..+-
T Consensus         8 k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           8 KELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            344467889999999999999988853 2357889999999999999999999999987531   11  11 24677777


Q ss_pred             HHhcCCCChHHHHHhhh
Q 025225          220 KGLLPHPLLRSKVKKDF  236 (256)
Q Consensus       220 ~~~~~~g~~~~a~~~~~  236 (256)
                      ..+...+++++|++...
T Consensus        87 ~~~~~~~~~~~A~~~~~  103 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYN  103 (128)
T ss_dssp             HHHHHTTCHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHH
Confidence            88888899999998443

>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=96.29  E-value=0.039  Score=38.40  Aligned_cols=64  Identities=6%  Similarity=-0.043  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          142 AYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       142 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      ...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.+|.+.|++++|.+.|++..+.
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3455566666777777777777777766532 124566777777777777777777777776654

>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=96.11  E-value=0.045  Score=41.81  Aligned_cols=116  Identities=11%  Similarity=0.033  Sum_probs=78.0

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HhhHHHHHH
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPD-----AYIYKDLIIALARTGKMNEAMQVWESMRKED-LFPD----SQTYTEVIR  185 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~-----~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~li~  185 (256)
                      +...|++++|++.+++..+..  +.+     ...++.+-..|...|++++|.+.|++..+.. -.++    ..++..+..
T Consensus        22 ~~~~g~~~~A~~~~~~aL~~~--~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~   99 (366)
T d1hz4a_          22 AINDGNPDEAERLAKLALEEL--PPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSE   99 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTC--CTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhhC--cCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHH
Confidence            457889999999998876653  222     3466777778888899999999988776521 1112    345566677


Q ss_pred             HHHHcCChhHHHHHHHHHHh----CCCC--CCh-hHHHHHHHHhcCCCChHHHHH
Q 025225          186 GFLKDGSPADAMNIYEDMIK----SPDP--PEE-LPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       186 ~~~~~g~~~~a~~~~~~M~~----~g~~--p~~-~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .+...|++..+...+.+...    .+..  +.. ..+..+-..+...|+++++..
T Consensus       100 ~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~  154 (366)
T d1hz4a_         100 ILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEA  154 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHH
Confidence            78888899988888876543    2222  211 244456667778888888776

>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=95.94  E-value=0.17  Score=38.40  Aligned_cols=152  Identities=11%  Similarity=-0.063  Sum_probs=100.0

Q ss_pred             HHhhcCCCcHHHHHHHHHHHhhcc-CCCcHH------HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCC----HHHHHHHH
Q 025225           81 LGLKRFKDDEEKLQKFIKTHVLRL-LKMDIV------AVLIELERQEETILAVKIFDIIRKQDWYQPD----AYIYKDLI  149 (256)
Q Consensus        81 ~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~------~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~y~~li  149 (256)
                      ..+...|+.++|+..+ +...... -.++..      .+-..+...|++++|...|.+..+...-.++    ..++..+.
T Consensus        20 ~~~~~~g~~~~A~~~~-~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~   98 (366)
T d1hz4a_          20 QVAINDGNPDEAERLA-KLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQS   98 (366)
T ss_dssp             HHHHHTTCHHHHHHHH-HHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHH-HHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHH
Confidence            4567899999998544 4443322 111111      2456777899999999999987653211122    34566777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHh----CCCC--CC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC----CCCCChhHHHHH
Q 025225          150 IALARTGKMNEAMQVWESMRK----EDLF--PD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS----PDPPEELPFRIL  218 (256)
Q Consensus       150 ~~~~~~g~~~~a~~~~~~m~~----~g~~--p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~p~~~t~~~l  218 (256)
                      ..+...|+++.+...+.+...    .+..  +. ...+..+-..+...|+++.+...+......    +.......+..+
T Consensus        99 ~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (366)
T d1hz4a_          99 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML  178 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence            788899999999999987653    1111  11 234556667788999999999999887653    233344555566


Q ss_pred             HHHhcCCCChHHHHH
Q 025225          219 LKGLLPHPLLRSKVK  233 (256)
Q Consensus       219 i~~~~~~g~~~~a~~  233 (256)
                      ...+...|...++..
T Consensus       179 ~~~~~~~~~~~~a~~  193 (366)
T d1hz4a_         179 IQCSLARGDLDNARS  193 (366)
T ss_dssp             HHHHHHHTCHHHHHH
T ss_pred             HHHHHhhhhHHHHHH
Confidence            666777777777665

>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=95.79  E-value=0.16  Score=35.04  Aligned_cols=75  Identities=11%  Similarity=0.111  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHH
Q 025225          143 YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLK  220 (256)
Q Consensus       143 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~  220 (256)
                      ..|+.+-.+|.+.|++++|...+++..+.. +.+...|..+-.+|...|++++|.+.|.+..+.  .|+.......+.
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~  139 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIF  139 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            457778888999999999999999988742 246788999999999999999999999999875  455444443333

>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=95.79  E-value=0.026  Score=38.47  Aligned_cols=99  Identities=12%  Similarity=-0.000  Sum_probs=48.3

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----------cCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHH
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----------TGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRG  186 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----------~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~  186 (256)
                      +.+.+++|.+.|+...+..  +-++.+|..+=.+|..          .+.+++|.+.|++..+.  .| +..+|..+=..
T Consensus         9 r~~~fe~A~~~~e~al~~~--P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l--~P~~~~a~~~lG~~   84 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhC--CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHh--cchhhHHHhhHHHH
Confidence            3444566666666655554  4444455444444432          23345566666655542  23 33455555444


Q ss_pred             HHHcC-----------ChhHHHHHHHHHHhCCCCCChhHHHHHHHHh
Q 025225          187 FLKDG-----------SPADAMNIYEDMIKSPDPPEELPFRILLKGL  222 (256)
Q Consensus       187 ~~~~g-----------~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~  222 (256)
                      |...|           .+++|.+.|++..+.  .|+..+|..-+..+
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~~~L~~~  129 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMT  129 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHHHHHHHH
Confidence            44432           234455555544433  45555555444444

>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=95.53  E-value=0.062  Score=37.31  Aligned_cols=66  Identities=14%  Similarity=0.066  Sum_probs=52.6

Q ss_pred             CHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH--hhhhhcCCC
Q 025225          176 DSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK--KDFEELFPE  242 (256)
Q Consensus       176 ~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~~~~p~  242 (256)
                      +...|+.+-..|.+.|++++|+..+++..+.. +-+...|..+-.+|.+.|++++|++  .....+.|+
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~  143 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE  143 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCC
Confidence            44567777888999999999999999998764 3467788899999999999999998  333344554

>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=95.36  E-value=0.18  Score=34.30  Aligned_cols=91  Identities=10%  Similarity=-0.053  Sum_probs=67.5

Q ss_pred             HHHHHH--HHHHHhcCCHHHHHHHHHHHHhC-CCCCC----------HhhHHHHHHHHHHcCChhHHHHHHHHHHhC---
Q 025225          143 YIYKDL--IIALARTGKMNEAMQVWESMRKE-DLFPD----------SQTYTEVIRGFLKDGSPADAMNIYEDMIKS---  206 (256)
Q Consensus       143 ~~y~~l--i~~~~~~g~~~~a~~~~~~m~~~-g~~p~----------~~t~~~li~~~~~~g~~~~a~~~~~~M~~~---  206 (256)
                      .+|..+  -..+...|++++|.+.|++-.+. .-.|+          ...|+.+-.+|.+.|++++|.+.+++..+.   
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            356655  44566779999999999998762 11122          367889999999999999999999887642   


Q ss_pred             --CCCCC-----hhHHHHHHHHhcCCCChHHHHH
Q 025225          207 --PDPPE-----ELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       207 --g~~p~-----~~t~~~li~~~~~~g~~~~a~~  233 (256)
                        ...|+     ...|+.+-.+|.+.|++++|++
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~  121 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALALDGLGRGAEAMP  121 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccccccccchhHHHHhhhHHHHHHHHHHHHHHH
Confidence              22232     2245667789999999999998

>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=95.00  E-value=0.057  Score=33.68  Aligned_cols=60  Identities=10%  Similarity=0.033  Sum_probs=35.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC----CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQD----WYQPD-AYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~----~~~p~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      .+=..+.+.|++++|...|++..+..    ...++ ..+++.+-.+|.+.|++++|.+.+++..+
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            34455666677777777666554331    01112 35666677777777777777777777665

>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=94.95  E-value=0.11  Score=35.08  Aligned_cols=80  Identities=15%  Similarity=0.059  Sum_probs=60.6

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC-----------CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH
Q 025225          119 QEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG-----------KMNEAMQVWESMRKEDLFPDSQTYTEVIRGF  187 (256)
Q Consensus       119 ~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g-----------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  187 (256)
                      .+.+++|+..|++..+..  +-+..+|..+=.+|...|           .+++|.+.|++..+  +.|+..+|..-+.-+
T Consensus        54 ~~~~~~Ai~~~~kAl~l~--P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~  129 (145)
T d1zu2a1          54 KQMIQEAITKFEEALLID--PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMT  129 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhc--chhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHH
Confidence            356789999999999886  677889988888887654           36888888888776  468887777666655


Q ss_pred             HHcCChhHHHHHHHHHHhCCC
Q 025225          188 LKDGSPADAMNIYEDMIKSPD  208 (256)
Q Consensus       188 ~~~g~~~~a~~~~~~M~~~g~  208 (256)
                            .+|.+++.+..+.|+
T Consensus       130 ------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         130 ------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             ------HTHHHHHHHHHHSSS
T ss_pred             ------HHHHHHHHHHHHHhc
Confidence                  467777777766654

>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=94.91  E-value=0.53  Score=35.94  Aligned_cols=111  Identities=6%  Similarity=-0.028  Sum_probs=80.4

Q ss_pred             HcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCCCHhhHHHHH-HHHHHcCChh
Q 025225          118 RQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTG--KMNEAMQVWESMRKEDLFPDSQTYTEVI-RGFLKDGSPA  194 (256)
Q Consensus       118 ~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~t~~~li-~~~~~~g~~~  194 (256)
                      ..|++++|+..++...+..  +-+...|..+-.++...+  +.++|...+++..+.. .++...+...+ ..+-..|+.+
T Consensus        85 ~~~~~~~al~~~~~~l~~~--pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~  161 (334)
T d1dcea1          85 SAALVKAELGFLESCLRVN--PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPA  161 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHH
T ss_pred             HHHHHHHHHHHHHHHHHhC--CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccH
Confidence            4456889999999998886  567788888877777765  4899999999988742 13455555444 5566689999


Q ss_pred             HHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHH
Q 025225          195 DAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKV  232 (256)
Q Consensus       195 ~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~  232 (256)
                      +|...+++..+... -+...|+.+-..+.+.|++++|.
T Consensus       162 ~Al~~~~~~i~~~p-~~~~a~~~l~~~~~~~~~~~~A~  198 (334)
T d1dcea1         162 EELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSG  198 (334)
T ss_dssp             HHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCHHHHH
Confidence            99999998877643 24566776666777766655543

>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=93.17  E-value=0.5  Score=28.97  Aligned_cols=60  Identities=8%  Similarity=0.009  Sum_probs=47.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCC-HhhHHHHHHHHHHcCChhHHHHHHHHHHhC
Q 025225          147 DLIIALARTGKMNEAMQVWESMRKE-----DLFPD-SQTYTEVIRGFLKDGSPADAMNIYEDMIKS  206 (256)
Q Consensus       147 ~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~M~~~  206 (256)
                      .+=..+.+.|++++|...|++..+.     ...++ ..+++.|-.+|.+.|++++|.+.+++..+.
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            4456678899999999999987652     12222 467888999999999999999999998876

>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=92.64  E-value=0.52  Score=31.04  Aligned_cols=59  Identities=24%  Similarity=0.092  Sum_probs=28.9

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 025225          113 LIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDL  173 (256)
Q Consensus       113 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  173 (256)
                      ++.+.+.|.-++-.++++++.+.+  +|++...-.+-.+|.+-|...++.+++.+..+.|+
T Consensus        93 Ld~lv~~~kkd~Ld~i~~~l~kn~--~i~~~~llkia~A~kkig~~re~nell~~ACe~G~  151 (161)
T d1wy6a1          93 LDILVIQGKRDKLEEIGREILKNN--EVSASILVAIANALRRVGDERDATTLLIEACKKGE  151 (161)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHC--C--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhccHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhH
Confidence            444445555555555555544443  44554555555555555555555555555554443

>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=92.47  E-value=1.6  Score=33.02  Aligned_cols=117  Identities=7%  Similarity=-0.033  Sum_probs=77.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCCCHHHHHHH---HHHH-------HhcCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHH
Q 025225          121 ETILAVKIFDIIRKQDWYQPDAYIYKDL---IIAL-------ARTGKMNEAMQVWESMRKEDLFP-DSQTYTEVIRGFLK  189 (256)
Q Consensus       121 ~~~~a~~~~~~m~~~~~~~p~~~~y~~l---i~~~-------~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~  189 (256)
                      ..++|+++++...+..  +-+...|+..   +..+       ...|.+++|..++++..+.  .| +...|..+-.++..
T Consensus        44 ~~~~al~~~~~~l~~~--P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~--~pk~~~~~~~~~~~~~~  119 (334)
T d1dcea1          44 LDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV--NPKSYGTWHHRCWLLSR  119 (334)
T ss_dssp             CSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHh--CCCcHHHHHHhhHHHHH
Confidence            3588999999888764  2233445432   2222       3345588999999988764  25 56677777777777


Q ss_pred             cCC--hhHHHHHHHHHHhCCCCCChhHHH-HHHHHhcCCCChHHHHHhhhhhcCCC
Q 025225          190 DGS--PADAMNIYEDMIKSPDPPEELPFR-ILLKGLLPHPLLRSKVKKDFEELFPE  242 (256)
Q Consensus       190 ~g~--~~~a~~~~~~M~~~g~~p~~~t~~-~li~~~~~~g~~~~a~~~~~~~~~p~  242 (256)
                      .++  .++|...+.+..+... ++...+. ..-..+...|..++|+.....-+.-+
T Consensus       120 ~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~  174 (334)
T d1dcea1         120 LPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN  174 (334)
T ss_dssp             CSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT
T ss_pred             hccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC
Confidence            664  7899999999887632 3444444 34467778899999998444444433

>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=91.44  E-value=2.4  Score=32.74  Aligned_cols=141  Identities=13%  Similarity=-0.004  Sum_probs=90.3

Q ss_pred             hHHHHHHHhhcCCCcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh
Q 025225           75 EALFVILGLKRFKDDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR  154 (256)
Q Consensus        75 ~~~~~i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~  154 (256)
                      .+..++..+.+.++...|++.+ .   +.+..-.+..+..++.+......+     .+...+ ...++..-..++..|-.
T Consensus        42 d~~rl~~~~v~l~~~~~avd~~-~---k~~~~~~~k~~~~~l~~~~e~~la-----~i~~~~-~~~~~d~l~~~v~~ye~  111 (336)
T d1b89a_          42 NFGRLASTLVHLGEYQAAVDGA-R---KANSTRTWKEVCFACVDGKEFRLA-----QMCGLH-IVVHADELEELINYYQD  111 (336)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHH-H---HHTCHHHHHHHHHHHHHTTCHHHH-----HHTTTT-TTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhhccHHHHHHHH-H---HcCCHHHHHHHHHHHHhCcHHHHH-----HHHHHH-hhcCHHHHHHHHHHHHH
Confidence            3444555666666666665322 1   222211222466666666655443     223333 45677777889999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHHhcCCCChHHHHH
Q 025225          155 TGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKGLLPHPLLRSKVK  233 (256)
Q Consensus       155 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  233 (256)
                      .|.+++...+++..... -.++...++-++..|++.+ .++..+.+...  .    +.....-+++.|-+.+.+.+++.
T Consensus       112 ~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~-~~kl~e~l~~~--s----~~y~~~k~~~~c~~~~l~~elv~  182 (336)
T d1b89a_         112 RGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK-PQKMREHLELF--W----SRVNIPKVLRAAEQAHLWAELVF  182 (336)
T ss_dssp             TTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC-HHHHHHHHHHH--S----TTSCHHHHHHHHHTTTCHHHHHH
T ss_pred             cCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC-hHHHHHHHHhc--c----ccCCHHHHHHHHHHcCChHHHHH
Confidence            99999999999986542 2457778899999999865 44444444433  2    23445678899999999988876

>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=89.69  E-value=1.3  Score=29.07  Aligned_cols=69  Identities=12%  Similarity=0.090  Sum_probs=57.5

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCC
Q 025225          140 PDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDP  209 (256)
Q Consensus       140 p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  209 (256)
                      .+..-.+-.++.+...|+-|+-.++++++.+ +-+|+....-.+-.+|-+-|...++-+++.+.-+.|++
T Consensus        84 ~~se~vdlALd~lv~~~kkd~Ld~i~~~l~k-n~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          84 TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             chHHHHHHHHHHHHHhccHHHHHHHHHHHHh-cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            4556677788899999999999999999776 44678888888999999999999999999998888874

>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=87.73  E-value=2  Score=26.65  Aligned_cols=46  Identities=17%  Similarity=0.217  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 025225          124 LAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRK  170 (256)
Q Consensus       124 ~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  170 (256)
                      ++.+-++.+.... ..|++..-.+.+.+|-+-+++.-|.++|+..+.
T Consensus        24 e~rrgmN~l~~~D-lVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~   69 (105)
T d1v54e_          24 ELRKGMNTLVGYD-LVPEPKIIDAALRACRRLNDFASAVRILEVVKD   69 (105)
T ss_dssp             HHHHHHHHHTTSS-BCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccc-cCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3444444444444 555555555555555555555555555555543

>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=87.70  E-value=0.18  Score=41.62  Aligned_cols=102  Identities=16%  Similarity=0.015  Sum_probs=53.7

Q ss_pred             HHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHHcCChh
Q 025225          116 LERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDS-QTYTEVIRGFLKDGSPA  194 (256)
Q Consensus       116 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~  194 (256)
                      +.+.|+.++|...+....+..   | ..++..+=..+...|++++|...|++..+.  .|+. ..|+.|=..|...|+..
T Consensus       130 ~~~~~~~~~A~~~~~~al~~~---~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~  203 (497)
T d1ya0a1         130 SNKQTHTSAIVKPQSSSCSYI---C-QHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHL  203 (497)
T ss_dssp             -------------CCHHHHHH---H-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHH
T ss_pred             HHhCCCHHHHHHHHHHHhCCC---H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHH
Confidence            344455555555444433221   1 234555566666677777777777776652  3543 56777777777777777


Q ss_pred             HHHHHHHHHHhCCCCCChhHHHHHHHHhcC
Q 025225          195 DAMNIYEDMIKSPDPPEELPFRILLKGLLP  224 (256)
Q Consensus       195 ~a~~~~~~M~~~g~~p~~~t~~~li~~~~~  224 (256)
                      +|...|.+-.... .|....+..|...+.+
T Consensus       204 ~A~~~y~ral~~~-~~~~~a~~nL~~~~~~  232 (497)
T d1ya0a1         204 TTIFYYCRSIAVK-FPFPAASTNLQKALSK  232 (497)
T ss_dssp             HHHHHHHHHHSSS-BCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCC-CCCHHHHHHHHHHHHH
Confidence            7777777766543 3556666666665543

>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=87.14  E-value=2.2  Score=26.42  Aligned_cols=64  Identities=16%  Similarity=0.194  Sum_probs=52.4

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHcCChhHHHHHHHHHHhCCCCCChhHHHHHHHH
Q 025225          157 KMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKDGSPADAMNIYEDMIKSPDPPEELPFRILLKG  221 (256)
Q Consensus       157 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~~~~~M~~~g~~p~~~t~~~li~~  221 (256)
                      +.-++.+-++.+-...+.|......+-+++|-+.+++.-|.++|+..+.. +.++...|..++.-
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilqe   84 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE   84 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHHH
Confidence            56677888888888889999999999999999999999999999987744 33456678777653

>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=84.76  E-value=6.9  Score=29.96  Aligned_cols=85  Identities=8%  Similarity=0.081  Sum_probs=56.8

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHHc
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMNEAMQVWESMRKEDLFPDSQTYTEVIRGFLKD  190 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  190 (256)
                      .++..|-..|.+++...+++......  .++...++-++..|++.+. +   ++.+.++..   .+..-..-+++.|-+.
T Consensus       104 ~~v~~ye~~~~~e~Li~~Le~~~~~~--~~~~~~~~~L~~lyak~~~-~---kl~e~l~~~---s~~y~~~k~~~~c~~~  174 (336)
T d1b89a_         104 ELINYYQDRGYFEELITMLEAALGLE--RAHMGMFTELAILYSKFKP-Q---KMREHLELF---WSRVNIPKVLRAAEQA  174 (336)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHTTST--TCCHHHHHHHHHHHHTTCH-H---HHHHHHHHH---STTSCHHHHHHHHHTT
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHcCC--ccchHHHHHHHHHHHHhCh-H---HHHHHHHhc---cccCCHHHHHHHHHHc
Confidence            47888888899999888888766443  6788888889998888752 3   344444431   1223345566777666


Q ss_pred             CChhHHHHHHHHHH
Q 025225          191 GSPADAMNIYEDMI  204 (256)
Q Consensus       191 g~~~~a~~~~~~M~  204 (256)
                      +-++++.-++.+|.
T Consensus       175 ~l~~elv~Ly~~~~  188 (336)
T d1b89a_         175 HLWAELVFLYDKYE  188 (336)
T ss_dssp             TCHHHHHHHHHHTT
T ss_pred             CChHHHHHHHHhcC
Confidence            66666666666654

>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=83.99  E-value=3.9  Score=26.53  Aligned_cols=63  Identities=14%  Similarity=0.212  Sum_probs=44.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCHH--HHHHHHHHHHhCCCCC
Q 025225          111 AVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALARTGKMN--EAMQVWESMRKEDLFP  175 (256)
Q Consensus       111 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~~g~~~--~a~~~~~~m~~~g~~p  175 (256)
                      .+|+-|..+|+.++|.+.++++....  ....+++..+..++-+.++-.  .+..++..+...|+-+
T Consensus        12 ~ll~EY~~~~D~~Ea~~~l~eL~~p~--~~~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~~~~~is   76 (129)
T d2nsza1          12 MLLKEYLLSGDISEAEHCLKELEVPH--FHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTIT   76 (129)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHHTCGG--GHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHhCCCHHHHHHHHHHcCCch--hhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHCCCCC
Confidence            58888888899999988888886332  224566666777776666543  3567888888865433

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=81.27  E-value=4.9  Score=25.73  Aligned_cols=111  Identities=7%  Similarity=-0.023  Sum_probs=62.0

Q ss_pred             CcHHHHHHHHHHHhhccCCCcHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHh----cCCHHHHHH
Q 025225           88 DDEEKLQKFIKTHVLRLLKMDIVAVLIELERQEETILAVKIFDIIRKQDWYQPDAYIYKDLIIALAR----TGKMNEAMQ  163 (256)
Q Consensus        88 ~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~y~~li~~~~~----~g~~~~a~~  163 (256)
                      +.++|+ .++....+.|.......|.  .....+.++|++.++...+.|    ++.....|=..|..    ..+.++|.+
T Consensus         8 d~~~A~-~~~~kaa~~g~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g----~~~a~~~Lg~~y~~g~~~~~d~~~A~~   80 (133)
T d1klxa_           8 DLKKAI-QYYVKACELNEMFGCLSLV--SNSQINKQKLFQYLSKACELN----SGNGCRFLGDFYENGKYVKKDLRKAAQ   80 (133)
T ss_dssp             HHHHHH-HHHHHHHHTTCTTHHHHHH--TCTTSCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             CHHHHH-HHHHHHHHCCChhhhhhhc--cccccCHHHHHHHHhhhhccc----chhhhhhHHHhhhhccccchhhHHHHH
Confidence            345555 3334444444332222232  123456778888888777777    34444444444433    356788888


Q ss_pred             HHHHHHhCCCCCCHhhHHHHHHHHHH----cCChhHHHHHHHHHHhCCC
Q 025225          164 VWESMRKEDLFPDSQTYTEVIRGFLK----DGSPADAMNIYEDMIKSPD  208 (256)
Q Consensus       164 ~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~M~~~g~  208 (256)
                      +|++-.+.|   +......|=..|.+    ..+.++|.++|++-.+.|.
T Consensus        81 ~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          81 YYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            888877764   33334444444444    3467778888877766653

>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=80.52  E-value=1.4  Score=28.68  Aligned_cols=61  Identities=18%  Similarity=0.135  Sum_probs=41.8

Q ss_pred             HHHHHHHc---CCHHHHHHHHHHHHhcCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 025225          112 VLIELERQ---EETILAVKIFDIIRKQDWYQPDA-YIYKDLIIALARTGKMNEAMQVWESMRKEDLFPD  176 (256)
Q Consensus       112 li~~~~~~---~~~~~a~~~~~~m~~~~~~~p~~-~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  176 (256)
                      .--++.++   .+.++|+.++++..+.+  ..+. ..+--|--+|.+.|++++|.+.++...+  +.|+
T Consensus        41 YAw~Lv~S~~~~d~~~gI~lLe~~~~~~--p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~--ieP~  105 (124)
T d2pqrb1          41 YAWGLIKSTDVNDERLGVKILTDIYKEA--ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERN  105 (124)
T ss_dssp             HHHHHHHSSCHHHHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HCTT
T ss_pred             HHHHHHcCCcHHHHHHHHHHHHHHHhcC--chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc--cCCC
Confidence            44445544   45678999999888664  2232 3444555668889999999999998887  3455