Citrus Sinensis ID: 042815

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-------
Protein Sequence
MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Secondary Structure (PSIPRED)
cccccccEEHHHHHHHHHcccccHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHHHHcHHHHHHcccccccHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccEEEEEEEEccccccEEEEEEcEEcccccEEEEccHHHHHHHHHcc
Coil and Loop (DISEMBL)
mmpprdattsSAMMLGLAkngkngmgVELFMSIekrgprpnavTFVGVLTAYGKIKIFGVTlmgiqpqnlwyYIDGQIDAWQAACQI
Flexible Loop (DISEMBL)
mmpprdattssAMMLGLAKNGKNGMGVELFMSiekrgprpnAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Low Complexity Region (SEG)
MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Disordered region (IsUnstruct)
*************************GVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAAC**
Disordered Region (DISOPRED)
**PPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Disordered Region (DISEMBL)
**********SAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Disordered Region (DISPRO)
**PPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVTLMGIQPQNLWYYIDGQIDAWQAACQI
Positional Conservation
no confident homologs detected

---

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	87	2.2.26 [Sep-21-2011]
Q9SJG6	559	Pentatricopeptide repeat-	yes	no	0.563	0.087	0.408	4e-05
Q9ZVF4	584	Pentatricopeptide repeat-	no	no	0.574	0.085	0.42	5e-05
Q9SIT7	697	Pentatricopeptide repeat-	no	no	0.597	0.074	0.384	6e-05
Q9SI53	630	Pentatricopeptide repeat-	no	no	0.724	0.1	0.361	7e-05
Q9LIE7	820	Pentatricopeptide repeat-	no	no	0.540	0.057	0.382	8e-05
Q3ECB8	467	Pentatricopeptide repeat-	no	no	0.574	0.107	0.42	0.0001
Q9C866	570	Pentatricopeptide repeat-	no	no	0.540	0.082	0.425	0.0001
Q5XEY7	477	Pentatricopeptide repeat-	no	no	0.574	0.104	0.44	0.0003
Q9LR69	609	Pentatricopeptide repeat-	no	no	0.597	0.085	0.365	0.0005
Q9LSB8	687	Putative pentatricopeptid	no	no	0.574	0.072	0.36	0.0005

>sp|Q9SJG6|PP200_ARATH Pentatricopeptide repeat-containing protein At2g42920, chloroplastic OS=Arabidopsis thaliana GN=PCMP-E75 PE=2 SV=1

 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 33/49 (67%)

Query: 3   PPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           P +  +  ++M+LGLA NG     ++LF  +E+ G  P++V+F+GVLTA
Sbjct: 320 PKKQLSCWNSMILGLANNGFEERAMDLFSELERSGLEPDSVSFIGVLTA 368

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVF4|PP140_ARATH Pentatricopeptide repeat-containing protein At2g01510, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H37 PE=3 SV=1

 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  R+  + S M++G A NG +   + LF +++  G RPN VTF+GVL+A
Sbjct: 271 MKQRNVVSWSTMIVGYAMNGDSREALTLFTTMQNEGLRPNYVTFLGVLSA 320

Arabidopsis thaliana (taxid: 3702)

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

 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 33/52 (63%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYG 53
           M  RD  + +AM++G A+NG     +ELF  + + G +P+ +T +GVL+A G
Sbjct: 453 MMERDCVSWNAMIIGFAQNGYGNEALELFREMLESGEKPDHITMIGVLSACG 504

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SI53|PP147_ARATH Pentatricopeptide repeat-containing protein At2g03880, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H44 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 9/72 (12%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVT 61
           M  RD  T S M+ GLA+NG +   ++LF  ++  G +PN +T VGVL        F  +
Sbjct: 319 MKERDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYITIVGVL--------FACS 370

Query: 62  LMGIQPQNLWYY 73
             G+  ++ WYY
Sbjct: 371 HAGLL-EDGWYY 381

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIE7|PP246_ARATH Pentatricopeptide repeat-containing protein At3g22150, chloroplastic OS=Arabidopsis thaliana GN=PCMP-E95 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/47 (38%), Positives = 33/47 (70%)

Query: 5   RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           R++ T + M+LG  ++G     + LF+S+++ G +P+A+TFV VL+A
Sbjct: 585 RNSVTYTTMILGYGQHGMGERAISLFLSMQESGIKPDAITFVAVLSA 631

Arabidopsis thaliana (taxid: 3702)

>sp|Q3ECB8|PP128_ARATH Pentatricopeptide repeat-containing protein At1g77170 OS=Arabidopsis thaliana GN=PCMP-E21 PE=2 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  R+  + S+M++G A NG     +E F  + + G RPN +TFVGVL+A
Sbjct: 281 MRQRNVVSWSSMIVGYAANGNTLEALECFRQMREFGVRPNKITFVGVLSA 330

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C866|PPR65_ARATH Pentatricopeptide repeat-containing protein At1g31430 OS=Arabidopsis thaliana GN=PCMP-E55 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/47 (42%), Positives = 32/47 (68%)

Query: 5   RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           RD  + ++++ GLA NG +G  ++L+  +E  G R +A+TFV VLTA
Sbjct: 343 RDTASWTSLIYGLAMNGMSGRALDLYYEMENVGVRLDAITFVAVLTA 389

Arabidopsis thaliana (taxid: 3702)

>sp|Q5XEY7|PP309_ARATH Pentatricopeptide repeat-containing protein At4g14170 OS=Arabidopsis thaliana GN=PCMP-E17 PE=2 SV=2

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  RD  + S+++LG   +G   M  +LF  + K G  PNAVTF+GVL+A
Sbjct: 296 MSRRDVISWSSLILGYGLDGDVVMSFKLFDEMLKEGIEPNAVTFLGVLSA 345

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LR69|PPR8_ARATH Pentatricopeptide repeat-containing protein At1g03540 OS=Arabidopsis thaliana GN=PCMP-E4 PE=2 SV=1

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 32/52 (61%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYG 53
           M  R+  T +AM+  LA+NG+    V  F  + K+G +P+ ++F+ +LTA G
Sbjct: 423 MSIRNMITWNAMLSALAQNGRGEEAVSFFNDMVKKGIKPDYISFIAILTACG 474

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSB8|PP235_ARATH Putative pentatricopeptide repeat-containing protein At3g15930 OS=Arabidopsis thaliana GN=PCMP-E51 PE=3 SV=2

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 33/50 (66%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  RD  T +AM++GLA NG+    +++F  ++    +P+ +T++GVL+A
Sbjct: 429 MDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQPDDITYLGVLSA 478

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	87
357519199	515	Pentatricopeptide repeat protein [Medica	0.770	0.130	0.550	9e-12
296088887	575	unnamed protein product [Vitis vinifera]	0.540	0.081	0.638	2e-10
357466867	629	Pentatricopeptide repeat protein [Medica	0.770	0.106	0.536	2e-10
356544269	522	PREDICTED: pentatricopeptide repeat-cont	0.701	0.116	0.557	5e-10
296085643	848	unnamed protein product [Vitis vinifera]	0.528	0.054	0.630	7e-10
255580411	392	pentatricopeptide repeat-containing prot	0.574	0.127	0.6	5e-09
356498888	552	PREDICTED: putative pentatricopeptide re	0.597	0.094	0.461	3e-05
125555946	530	hypothetical protein OsI_23585 [Oryza sa	0.574	0.094	0.46	3e-05
115468780	530	Os06g0597500 [Oryza sativa Japonica Grou	0.574	0.094	0.46	3e-05
218198170	563	hypothetical protein OsI_22944 [Oryza sa	0.724	0.111	0.375	4e-05

>gi|357519199|ref|XP_003629888.1| Pentatricopeptide repeat protein [Medicago truncatula] gi|355523910|gb|AET04364.1| Pentatricopeptide repeat protein [Medicago truncatula]

 Score = 74.3 bits (181), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/69 (55%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVT 61
           MP +D  T SAM+LGLA NG N M +ELF  +EK GP+PN VTFVGVLTA     +FG +
Sbjct: 283 MPVKDVATWSAMILGLAINGNNKMALELFEKMEKVGPKPNEVTFVGVLTACNHKSLFGES 342

Query: 62  --LMGIQPQ 68
             L GI  +
Sbjct: 343 ARLFGIMSE 351

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088887|emb|CBI38431.3| unnamed protein product [Vitis vinifera]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 37/47 (78%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGV 48
           MP +D T  S+M+LGLA NG N MG+ELF  +E RGPRPNA+TF+GV
Sbjct: 422 MPLKDVTAWSSMILGLAINGNNEMGLELFHEMETRGPRPNAITFIGV 468

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357466867|ref|XP_003603718.1| Pentatricopeptide repeat protein [Medicago truncatula] gi|355492766|gb|AES73969.1| Pentatricopeptide repeat protein [Medicago truncatula]

 Score = 69.7 bits (169), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/69 (53%), Positives = 45/69 (65%), Gaps = 2/69 (2%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVT 61
           M  +D  T SAM+LGLA NG N M +ELF  +EK GP+PN VTFVGVLTA     +FG +
Sbjct: 319 MLVKDVATWSAMILGLAINGNNKMALELFEKMEKVGPKPNEVTFVGVLTACNHKSLFGES 378

Query: 62  --LMGIQPQ 68
             L GI  +
Sbjct: 379 SRLFGIMSE 387

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356544269|ref|XP_003540576.1| PREDICTED: pentatricopeptide repeat-containing protein At5g66520-like [Glycine max]

 Score = 68.6 bits (166), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 34/61 (55%), Positives = 40/61 (65%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVT 61
           M  +D    SAM+LGLA N KN   +ELF  +EK GPRPNAVTF+GVLTA     +FG  
Sbjct: 292 MKTKDVAAWSAMVLGLAINAKNQEALELFEEMEKVGPRPNAVTFIGVLTACNHKDLFGEA 351

Query: 62  L 62
           L
Sbjct: 352 L 352

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085643|emb|CBI29442.3| unnamed protein product [Vitis vinifera]

 Score = 68.2 bits (165), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 29/46 (63%), Positives = 36/46 (78%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVG 47
           MP +D T  S+M+LGLA NG N MG+ELF  +E RGPRPNA+TF+G
Sbjct: 386 MPLKDVTAWSSMILGLAINGNNEMGLELFHEMETRGPRPNAITFIG 431

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255580411|ref|XP_002531032.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223529385|gb|EEF31349.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score = 65.1 bits (157), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 30/50 (60%), Positives = 39/50 (78%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  +D TT SAM+LGLA NG+N  G+ LF  +E++GP+ NAVTF+GVLTA
Sbjct: 285 MQYKDVTTWSAMILGLAINGENHRGIGLFAEMERKGPKANAVTFMGVLTA 334

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498888|ref|XP_003518279.1| PREDICTED: putative pentatricopeptide repeat-containing protein At5g37570-like [Glycine max]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/52 (46%), Positives = 35/52 (67%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYG 53
           M  RD  T SAM+   A++GK+   ++LF+ ++K G +PN VTF+GVL A G
Sbjct: 368 MRYRDVYTYSAMIAAFAEHGKSQDAIDLFLKMQKEGLKPNQVTFIGVLNACG 419

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125555946|gb|EAZ01552.1| hypothetical protein OsI_23585 [Oryza sativa Indica Group]

 Score = 52.4 bits (124), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/50 (46%), Positives = 35/50 (70%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  RDAT  +A++ GLA NG+ G  +ELF  +++   +P+ VTF+GVL+A
Sbjct: 342 MQGRDATAWTAIICGLATNGQAGRALELFQDMQRSKVKPDGVTFIGVLSA 391

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115468780|ref|NP_001057989.1| Os06g0597500 [Oryza sativa Japonica Group] gi|50725579|dbj|BAD33047.1| PPR-repeat protein-like [Oryza sativa Japonica Group] gi|113596029|dbj|BAF19903.1| Os06g0597500 [Oryza sativa Japonica Group] gi|125597760|gb|EAZ37540.1| hypothetical protein OsJ_21869 [Oryza sativa Japonica Group]

 Score = 52.4 bits (124), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/50 (46%), Positives = 35/50 (70%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
           M  RDAT  +A++ GLA NG+ G  +ELF  +++   +P+ VTF+GVL+A
Sbjct: 342 MQGRDATAWTAIICGLATNGQAGRALELFQDMQRSKVKPDGVTFIGVLSA 391

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218198170|gb|EEC80597.1| hypothetical protein OsI_22944 [Oryza sativa Indica Group]

 Score = 52.4 bits (124), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 9/72 (12%)

Query: 2   MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGVT 61
           MP RD  + S M+ GLA+NG++   +++F  ++  GPRPN +T VGVL        F  +
Sbjct: 286 MPQRDVISWSTMISGLAQNGRSIEALKVFDMMKSEGPRPNHITMVGVL--------FACS 337

Query: 62  LMGIQPQNLWYY 73
             G+  ++ WYY
Sbjct: 338 HAGLV-EDGWYY 348

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

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	87
TAIR|locus:2045580	559	AT2G42920 [Arabidopsis thalian	0.563	0.087	0.408	6.9e-05
TAIR|locus:2054131	697	SLO2 "AT2G13600" [Arabidopsis	0.597	0.074	0.384	0.00015
TAIR|locus:2206164	570	AT1G31430 [Arabidopsis thalian	0.540	0.082	0.425	0.00019
TAIR|locus:2049562	584	AT2G01510 "AT2G01510" [Arabido	0.574	0.085	0.42	0.0002
TAIR|locus:2056794	630	REME1 "required for efficiency	0.574	0.079	0.44	0.00022
TAIR|locus:2195980	467	AT1G77170 "AT1G77170" [Arabido	0.574	0.107	0.42	0.00024
TAIR|locus:2090444	820	AT3G22150 "AT3G22150" [Arabido	0.540	0.057	0.382	0.00038

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

 Score = 105 (42.0 bits), Expect = 6.9e-05, P = 6.9e-05
 Identities = 20/49 (40%), Positives = 33/49 (67%)

Query:     3 PPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
             P +  +  ++M+LGLA NG     ++LF  +E+ G  P++V+F+GVLTA
Sbjct:   320 PKKQLSCWNSMILGLANNGFEERAMDLFSELERSGLEPDSVSFIGVLTA 368

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 103 (41.3 bits), Expect = 0.00015, P = 0.00015
 Identities = 20/52 (38%), Positives = 33/52 (63%)

Query:     2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYG 53
             M  RD  + +AM++G A+NG     +ELF  + + G +P+ +T +GVL+A G
Sbjct:   453 MMERDCVSWNAMIIGFAQNGYGNEALELFREMLESGEKPDHITMIGVLSACG 504

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2206164 AT1G31430 [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 0.00019, P = 0.00019
 Identities = 20/47 (42%), Positives = 32/47 (68%)

Query:     5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
             RD  + ++++ GLA NG +G  ++L+  +E  G R +A+TFV VLTA
Sbjct:   343 RDTASWTSLIYGLAMNGMSGRALDLYYEMENVGVRLDAITFVAVLTA 389

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2049562 AT2G01510 "AT2G01510" [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 0.00020, P = 0.00020
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query:     2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
             M  R+  + S M++G A NG +   + LF +++  G RPN VTF+GVL+A
Sbjct:   271 MKQRNVVSWSTMIVGYAMNGDSREALTLFTTMQNEGLRPNYVTFLGVLSA 320

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2056794 REME1 "required for efficiency of mitochondrial editing 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 0.00022, P = 0.00022
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query:     2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
             M  RD  T S M+ GLA+NG +   ++LF  ++  G +PN +T VGVL A
Sbjct:   319 MKERDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYITIVGVLFA 368

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

TAIR|locus:2195980 AT1G77170 "AT1G77170" [Arabidopsis thaliana (taxid:3702)]

 Score = 99 (39.9 bits), Expect = 0.00024, P = 0.00024
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query:     2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
             M  R+  + S+M++G A NG     +E F  + + G RPN +TFVGVL+A
Sbjct:   281 MRQRNVVSWSSMIVGYAANGNTLEALECFRQMREFGVRPNKITFVGVLSA 330

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2090444 AT3G22150 "AT3G22150" [Arabidopsis thaliana (taxid:3702)]

 Score = 100 (40.3 bits), Expect = 0.00038, P = 0.00038
 Identities = 18/47 (38%), Positives = 33/47 (70%)

Query:     5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
             R++ T + M+LG  ++G     + LF+S+++ G +P+A+TFV VL+A
Sbjct:   585 RNSVTYTTMILGYGQHGMGERAISLFLSMQESGIKPDAITFVAVLSA 631


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.137   0.425    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       87        87   0.00091  102 3  11 22  0.44    29
                                                     29  0.48    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  534 (57 KB)
  Total size of DFA:  110 KB (2074 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.97u 0.19s 9.16t   Elapsed:  00:00:00
  Total cpu time:  8.97u 0.19s 9.16t   Elapsed:  00:00:00
  Start:  Tue May 21 03:23:00 2013   End:  Tue May 21 03:23:00 2013

GO:0016556 "mRNA modification" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	87
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-05
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-04

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

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 5   RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK 54
           +D  + + ++ G   +GK  M VELF  + + G  P+ VTF+ +L A  +
Sbjct: 552 KDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSR 601

Length = 857

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

 Score = 38.7 bits (90), Expect = 8e-05
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 1   MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA 51
            MP ++  + +A++ G   +G+    VE+F  +   G  PN VTF+ VL+A
Sbjct: 385 RMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSA 435

Length = 697

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

 Score = 35.5 bits (83), Expect = 2e-04
 Identities = 13/43 (30%), Positives = 23/43 (53%)

Query: 12 AMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK 54
           ++ G  K GK    ++LF  ++KRG +PN  T+  ++    K
Sbjct: 8  TLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	87
PF13041	50	PPR_2: PPR repeat family	99.88
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.86
PLN03077	857	Protein ECB2; Provisional	99.82
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.82
PLN03077	857	Protein ECB2; Provisional	99.81
PLN03218	1060	maturation of RBCL 1; Provisional	99.76
PLN03218	1060	maturation of RBCL 1; Provisional	99.76
PF12854	34	PPR_1: PPR repeat	99.49
PF13041	50	PPR_2: PPR repeat family	99.48
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.45
PF13812	34	PPR_3: Pentatricopeptide repeat domain	99.31
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	99.25
PF12854	34	PPR_1: PPR repeat	99.19
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.89
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.5
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.47
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.42
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.2
KOG4422	625	consensus Uncharacterized conserved protein [Funct	97.97
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.92
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.81
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.81
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.64
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.61
PRK11788	389	tetratricopeptide repeat protein; Provisional	97.54
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.42
PRK11788	389	tetratricopeptide repeat protein; Provisional	97.42
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.09
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.97
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.92
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	96.64
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.55
KOG3941	406	consensus Intermediate in Toll signal transduction	96.42
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	96.39
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	96.02
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	95.88
PF13428	44	TPR_14: Tetratricopeptide repeat	95.75
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.56
KOG2003	840	consensus TPR repeat-containing protein [General f	95.53
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.52
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	95.27
PRK15359	144	type III secretion system chaperone protein SscB;	95.04
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.69
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	94.65
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	94.54
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	94.31
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	94.19
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	94.18
KOG3941	406	consensus Intermediate in Toll signal transduction	93.99
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.64
TIGR02552	135	LcrH_SycD type III secretion low calcium response	93.53
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	93.52
PRK10564	303	maltose regulon periplasmic protein; Provisional	93.29
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.19
TIGR02552	135	LcrH_SycD type III secretion low calcium response	93.09
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	92.94
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.88
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	92.82
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.58
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	92.56
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	92.51
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	92.35
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	92.32
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	92.16
PF13371	73	TPR_9: Tetratricopeptide repeat	91.83
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	91.81
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	91.42
PF13431	34	TPR_17: Tetratricopeptide repeat	91.39
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	90.9
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	90.87
PF13762	145	MNE1: Mitochondrial splicing apparatus component	90.79
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	90.76
PF02607	79	B12-binding_2: B12 binding domain; InterPro: IPR00	90.53
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	90.47
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	90.28
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	90.23
PRK15359	144	type III secretion system chaperone protein SscB;	90.02
KOG4570	418	consensus Uncharacterized conserved protein [Funct	89.91
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	89.85
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	89.79
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	89.64
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	89.48
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	88.89
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	88.87
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	88.71
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	88.33
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	88.17
PRK12370	553	invasion protein regulator; Provisional	88.15
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	87.99
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	87.52
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	87.5
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	87.3
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	87.24
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	87.16
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	87.04
PRK11189	296	lipoprotein NlpI; Provisional	86.74
PF07443	55	HARP: HepA-related protein (HARP); InterPro: IPR01	86.67
PF12688	120	TPR_5: Tetratrico peptide repeat	86.47
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	85.92
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	85.8
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	85.67
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	85.67
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	85.15
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	85.03
PRK10370	198	formate-dependent nitrite reductase complex subuni	84.89
KOG2047	835	consensus mRNA splicing factor [RNA processing and	84.76
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	84.51
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	84.37
PF02847	113	MA3: MA3 domain; InterPro: IPR003891 This entry re	83.94
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	83.88
PRK12370	553	invasion protein regulator; Provisional	83.82
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	83.66
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	83.56
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	83.38
COG4003	98	Uncharacterized protein conserved in archaea [Func	83.17
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	83.07
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	82.99
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	82.83
PRK14574	822	hmsH outer membrane protein; Provisional	82.83
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	82.72
KOG0547	606	consensus Translocase of outer mitochondrial membr	80.95
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	80.86
KOG1915	677	consensus Cell cycle control protein (crooked neck	80.38
PRK14574	822	hmsH outer membrane protein; Provisional	80.23

>PF13041 PPR_2: PPR repeat family

Probab=99.88  E-value=1.1e-22  Score=97.26  Aligned_cols=50  Identities=28%  Similarity=0.482  Sum_probs=49.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK   54 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~   54 (87)
                      ||+++||+||.+|++.|++++|.++|++|.+.|+.||..||+++|++||+
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            89999999999999999999999999999999999999999999999986

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

Probab=99.86  E-value=1e-21  Score=133.57  Aligned_cols=84  Identities=23%  Similarity=0.351  Sum_probs=79.9

Q ss_pred             CCCCCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchh
Q 042815            1 MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQI   78 (87)
Q Consensus         1 ~m~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~   78 (87)
                      +|++||+++||+||.+|+++|+.++|+++|++|...|+.||..||+++|.+|++.|.+++  ++|+.|..+  .|+.|+.
T Consensus       385 ~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~--~g~~p~~  462 (697)
T PLN03081        385 RMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEN--HRIKPRA  462 (697)
T ss_pred             hCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHh--cCCCCCc
Confidence            478899999999999999999999999999999999999999999999999999999999  999999876  5999999


Q ss_pred             hhhhcccc
Q 042815           79 DAWQAACQ   86 (87)
Q Consensus        79 ~~~~~~~~   86 (87)
                      .+|+++++
T Consensus       463 ~~y~~li~  470 (697)
T PLN03081        463 MHYACMIE  470 (697)
T ss_pred             cchHhHHH
Confidence            99999875

>PLN03077 Protein ECB2; Provisional

Probab=99.82  E-value=2.6e-20  Score=128.99  Aligned_cols=81  Identities=22%  Similarity=0.432  Sum_probs=77.2

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAW   81 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~   81 (87)
                      +||+++||+||.+|+++|+.++|+++|++|.+.|+.||..||+++|.+|++.|.+++  ++|+.|...  .|+.|+..+|
T Consensus       551 ~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~--~gi~P~~~~y  628 (857)
T PLN03077        551 EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEK--YSITPNLKHY  628 (857)
T ss_pred             CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHH--hCCCCchHHH
Confidence            689999999999999999999999999999999999999999999999999999999  999999965  5999999999


Q ss_pred             hcccc
Q 042815           82 QAACQ   86 (87)
Q Consensus        82 ~~~~~   86 (87)
                      ++++.
T Consensus       629 ~~lv~  633 (857)
T PLN03077        629 ACVVD  633 (857)
T ss_pred             HHHHH
Confidence            98874

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

Probab=99.82  E-value=3.4e-20  Score=126.24  Aligned_cols=83  Identities=16%  Similarity=0.198  Sum_probs=79.2

Q ss_pred             CCCCCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchh
Q 042815            1 MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQI   78 (87)
Q Consensus         1 ~m~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~   78 (87)
                      +|+++|+++||+||.+|+++|++++|.++|++|...|+.||..||++++++|++.|.++.  ++++.|.+.   |+.||.
T Consensus       284 ~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~---g~~~d~  360 (697)
T PLN03081        284 GMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRT---GFPLDI  360 (697)
T ss_pred             hCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHh---CCCCCe
Confidence            488999999999999999999999999999999999999999999999999999999999  999999987   999999


Q ss_pred             hhhhcccc
Q 042815           79 DAWQAACQ   86 (87)
Q Consensus        79 ~~~~~~~~   86 (87)
                      .+||+++.
T Consensus       361 ~~~~~Li~  368 (697)
T PLN03081        361 VANTALVD  368 (697)
T ss_pred             eehHHHHH
Confidence            99999874

>PLN03077 Protein ECB2; Provisional

Probab=99.81  E-value=9.6e-20  Score=126.17  Aligned_cols=83  Identities=23%  Similarity=0.326  Sum_probs=79.4

Q ss_pred             CCCCCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchh
Q 042815            1 MMPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQI   78 (87)
Q Consensus         1 ~m~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~   78 (87)
                      +|++||.++||+||.+|+++|++++|+++|++|...|+.||..||+++|.+|++.|+++.  +++..|.+.   |+.||.
T Consensus       247 ~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~---g~~~d~  323 (857)
T PLN03077        247 RMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT---GFAVDV  323 (857)
T ss_pred             cCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHh---CCccch
Confidence            488999999999999999999999999999999999999999999999999999999998  889988887   999999


Q ss_pred             hhhhcccc
Q 042815           79 DAWQAACQ   86 (87)
Q Consensus        79 ~~~~~~~~   86 (87)
                      .+||++++
T Consensus       324 ~~~n~Li~  331 (857)
T PLN03077        324 SVCNSLIQ  331 (857)
T ss_pred             HHHHHHHH
Confidence            99999875

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.76  E-value=2.3e-18  Score=121.26  Aligned_cols=79  Identities=16%  Similarity=0.228  Sum_probs=67.5

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAW   81 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~   81 (87)
                      .||+++||+||.+|++.|++++|.++|++|...|+.||..||+++|.+|++.|+++.  ++|..|.+.   |+.||..+|
T Consensus       716 ~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~---Gi~pd~~ty  792 (1060)
T PLN03218        716 RPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKED---GIKPNLVMC  792 (1060)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc---CCCCCHHHH
Confidence            578888888888888888888888888888888888888888888888888888888  888888877   888888888


Q ss_pred             hccc
Q 042815           82 QAAC   85 (87)
Q Consensus        82 ~~~~   85 (87)
                      ++++
T Consensus       793 nsLI  796 (1060)
T PLN03218        793 RCIT  796 (1060)
T ss_pred             HHHH
Confidence            8775

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.76  E-value=2.3e-18  Score=121.31  Aligned_cols=78  Identities=18%  Similarity=0.221  Sum_probs=45.2

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQ   82 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~   82 (87)
                      ||.++||+||.+|++.|++++|.++|++|...|+.||..||+++|.+|++.|++++  .+|+.|...   |+.||..+||
T Consensus       470 pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~---Gv~PD~vTYn  546 (1060)
T PLN03218        470 ADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK---NVKPDRVVFN  546 (1060)
T ss_pred             CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHc---CCCCCHHHHH
Confidence            55555555555555555555555555555555555555555555555555555555  555555554   5555555555


Q ss_pred             ccc
Q 042815           83 AAC   85 (87)
Q Consensus        83 ~~~   85 (87)
                      ++|
T Consensus       547 sLI  549 (1060)
T PLN03218        547 ALI  549 (1060)
T ss_pred             HHH
Confidence            554

>PF12854 PPR_1: PPR repeat

Probab=99.49  E-value=3.2e-14  Score=62.66  Aligned_cols=32  Identities=25%  Similarity=0.366  Sum_probs=30.2

Q ss_pred             CCCcHhHHHHHHHHHHhcCCchhHHHHHHHHH
Q 042815            3 PPRDATTSSAMMLGLAKNGKNGMGVELFMSIE   34 (87)
Q Consensus         3 ~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~   34 (87)
                      -+||++|||+||.+||+.|++++|.++|++|+
T Consensus         3 ~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    3 CEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            36999999999999999999999999999984

>PF13041 PPR_2: PPR repeat family

Probab=99.48  E-value=3.1e-14  Score=67.70  Aligned_cols=44  Identities=18%  Similarity=0.258  Sum_probs=42.3

Q ss_pred             CCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhhcccc
Q 042815           40 PNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQAACQ   86 (87)
Q Consensus        40 pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~~~~~   86 (87)
                      ||.+||+++|++|++.|++++  ++|++|.++   |+.||..||+++++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~---g~~P~~~Ty~~li~   46 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKR---GIKPDSYTYNILIN   46 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHc---CCCCCHHHHHHHHH
Confidence            899999999999999999999  999999998   99999999999875

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.45  E-value=1.8e-13  Score=60.00  Aligned_cols=35  Identities=31%  Similarity=0.546  Sum_probs=33.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNA   42 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~   42 (87)
                      ++||+||.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            48999999999999999999999999999999984

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=99.31  E-value=4.4e-12  Score=55.38  Aligned_cols=34  Identities=26%  Similarity=0.498  Sum_probs=32.6

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP   40 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p   40 (87)
                      +++||++|.+|++.|++++|.++|++|.+.|++|
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            4699999999999999999999999999999998

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

Probab=99.25  E-value=8.8e-12  Score=53.27  Aligned_cols=31  Identities=26%  Similarity=0.440  Sum_probs=29.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCC
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGP   38 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~   38 (87)
                      ++||+||++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            5899999999999999999999999998875

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.

>PF12854 PPR_1: PPR repeat

Probab=99.19  E-value=2.4e-11  Score=53.34  Aligned_cols=32  Identities=25%  Similarity=0.372  Sum_probs=29.8

Q ss_pred             cCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815           36 RGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus        36 ~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .|+.||.+||+++|+++|+.|++++  ++|++|.
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            4899999999999999999999999  9998884

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.89  E-value=4.8e-09  Score=68.78  Aligned_cols=79  Identities=20%  Similarity=0.291  Sum_probs=64.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHH-------------------------------HHHHcCCCCCHhhHHHHHHHHc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFM-------------------------------SIEKRGPRPNAVTFVGVLTAYG   53 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~-------------------------------~m~~~g~~pd~~t~~~ll~~~~   53 (87)
                      ++--+|.+||.|.|+--..|+|.++|+                               +|....++||..|||+++++.+
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl~TfNalL~c~a  284 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNLFTFNALLSCAA  284 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCchHhHHHHHHHHH
Confidence            345788999999998777777777665                               4556778999999999999999


Q ss_pred             ccchhHH------HHHHhchhcccccccchhhhhhcccc
Q 042815           54 KIKIFGV------TLMGIQPQNLWYYIDGQIDAWQAACQ   86 (87)
Q Consensus        54 ~~~~~~~------~~~~~m~~~~~~g~~~~~~~~~~~~~   86 (87)
                      +.|+++.      +++.+|+.-   |++|+..+|.-+|.
T Consensus       285 kfg~F~~ar~aalqil~EmKei---GVePsLsSyh~iik  320 (625)
T KOG4422|consen  285 KFGKFEDARKAALQILGEMKEI---GVEPSLSSYHLIIK  320 (625)
T ss_pred             HhcchHHHHHHHHHHHHHHHHh---CCCcchhhHHHHHH
Confidence            9997766      788888887   99999998877664

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.50  E-value=1.1e-07  Score=41.01  Aligned_cols=33  Identities=15%  Similarity=0.129  Sum_probs=30.3

Q ss_pred             hhHHHHHHHHcccchhHH--HHHHhchhcccccccchh
Q 042815           43 VTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQI   78 (87)
Q Consensus        43 ~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~   78 (87)
                      .||+++|++|++.|++++  ++|+.|...   |+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~---g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLER---GIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHc---CCCCCC
Confidence            489999999999999999  999999987   999873

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.

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

Probab=98.47  E-value=9.5e-07  Score=48.50  Aligned_cols=73  Identities=14%  Similarity=0.134  Sum_probs=62.6

Q ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHcCC-CCCHhhHHHHHHHHcccch----hHH------HHHHhchhcccccccchhh
Q 042815           11 SAMMLGLAKNGKNGMGVELFMSIEKRGP-RPNAVTFVGVLTAYGKIKI----FGV------TLMGIQPQNLWYYIDGQID   79 (87)
Q Consensus        11 ~~li~~~~~~g~~~~a~~l~~~m~~~g~-~pd~~t~~~ll~~~~~~~~----~~~------~~~~~m~~~~~~g~~~~~~   79 (87)
                      ...|..+...+++.....+|+.++..|+ .|...+|+.+|++.++...    ++.      .+++.|...   ++.|+..
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~---~lKP~~e  105 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSN---KLKPNDE  105 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHh---ccCCcHH
Confidence            4567778888999999999999999999 9999999999999987532    222      788999877   8999999


Q ss_pred             hhhcccc
Q 042815           80 AWQAACQ   86 (87)
Q Consensus        80 ~~~~~~~   86 (87)
                      +||.+++
T Consensus       106 tYnivl~  112 (120)
T PF08579_consen  106 TYNIVLG  112 (120)
T ss_pred             HHHHHHH
Confidence            9998764

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 [, , ].

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.42  E-value=2.6e-07  Score=39.83  Aligned_cols=32  Identities=16%  Similarity=0.082  Sum_probs=29.3

Q ss_pred             HhhHHHHHHHHcccchhHH--HHHHhchhcccccccc
Q 042815           42 AVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDG   76 (87)
Q Consensus        42 ~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~   76 (87)
                      +.||+++|.+|++.|+++.  .+|+.|...   |++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~---gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQ---GVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCC
Confidence            3689999999999999999  999999987   8887

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

Probab=98.20  E-value=1.8e-06  Score=36.27  Aligned_cols=27  Identities=19%  Similarity=0.364  Sum_probs=25.2

Q ss_pred             hhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           43 VTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        43 ~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +||+++|++|++.|++++  ++|++|...
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~   29 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRER   29 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHC
Confidence            589999999999999999  999999876

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.

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.97  E-value=4.1e-05  Score=50.90  Aligned_cols=57  Identities=14%  Similarity=0.153  Sum_probs=51.4

Q ss_pred             CCcHhHHHHHHHHHHhcCCchh----HHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            4 PRDATTSSAMMLGLAKNGKNGM----GVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~----a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .||..|+|++++.-++.|+++.    |.+++.+|++-|+.|...+|-.+|.-.++.++..+
T Consensus       270 ~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  270 TPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             CCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh
Confidence            4899999999999999998765    56788999999999999999999999999988755

>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=97.92  E-value=5.5e-05  Score=45.98  Aligned_cols=82  Identities=13%  Similarity=0.099  Sum_probs=68.4

Q ss_pred             CCCcHhHHHHHHHHHHhc-----CCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH-----------------
Q 042815            3 PPRDATTSSAMMLGLAKN-----GKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV-----------------   60 (87)
Q Consensus         3 ~~~~~~~~~~li~~~~~~-----g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~-----------------   60 (87)
                      ..+|..+|..+|..|.+.     |++|=...-+..|.+-|+.-|..+|+.||+.+=+...+..                 
T Consensus        43 ~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~  122 (228)
T PF06239_consen   43 QAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECA  122 (228)
T ss_pred             ccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHH
Confidence            357888999999999875     7778788888999999999999999999999876332211                 


Q ss_pred             -HHHHhchhcccccccchhhhhhccccC
Q 042815           61 -TLMGIQPQNLWYYIDGQIDAWQAACQI   87 (87)
Q Consensus        61 -~~~~~m~~~~~~g~~~~~~~~~~~~~i   87 (87)
                       .++++|...   |+-||..++..+++|
T Consensus       123 i~lL~qME~~---gV~Pd~Et~~~ll~i  147 (228)
T PF06239_consen  123 IDLLEQMENN---GVMPDKETEQMLLNI  147 (228)
T ss_pred             HHHHHHHHHc---CCCCcHHHHHHHHHH
Confidence             778899987   999999999988764

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

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

Probab=97.81  E-value=8.2e-05  Score=40.98  Aligned_cols=54  Identities=19%  Similarity=0.132  Sum_probs=45.1

Q ss_pred             CCCCcHhHHHHHHHHHHhcC--------CchhHHHHHHHHHHcCCCCCHhhHHHHHHHHccc
Q 042815            2 MPPRDATTSSAMMLGLAKNG--------KNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKI   55 (87)
Q Consensus         2 m~~~~~~~~~~li~~~~~~g--------~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~   55 (87)
                      +.-|++.+||.++.+-++..        +.-+.+.+|+.|...+++|+..||+.++.++.+.
T Consensus        56 i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen   56 ITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             CCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHh
Confidence            34688999999999988853        2456788999999999999999999999887653

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=97.81  E-value=5.5e-05  Score=50.12  Aligned_cols=61  Identities=15%  Similarity=0.098  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      |..++|..|.+.|..++++.+++.=...|+-||.+||+.+|+.+-+.|+...  .+...|...
T Consensus       105 t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQ  167 (429)
T PF10037_consen  105 THHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQ  167 (429)
T ss_pred             cHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHh
Confidence            4469999999999999999999998899999999999999999999999988  776666655

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 [].

>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=97.64  E-value=0.00024  Score=43.28  Aligned_cols=57  Identities=18%  Similarity=0.227  Sum_probs=49.1

Q ss_pred             CCcHhHHHHHHHHHHhc----------------CCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            4 PRDATTSSAMMLGLAKN----------------GKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~----------------g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ++|+.+||.||.-+-+.                .+-+-|++++++|...|+.||..|+..++..+++.+..-.
T Consensus        84 ~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~  156 (228)
T PF06239_consen   84 EKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMK  156 (228)
T ss_pred             cccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHH
Confidence            47899999999988763                2236789999999999999999999999999999887654

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

>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=97.61  E-value=0.00056  Score=38.33  Aligned_cols=78  Identities=13%  Similarity=0.181  Sum_probs=56.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHH---------------HcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIE---------------KRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~---------------~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      |..++.++|.++++.|+.+....+.++.=               ...+.|+..+..+++.+++..+++..  ++.+....
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            45567788888888888888877776531               12355778888888888888888877  77777777


Q ss_pred             cccccccchhhhhhccc
Q 042815           69 NLWYYIDGQIDAWQAAC   85 (87)
Q Consensus        69 ~~~~g~~~~~~~~~~~~   85 (87)
                      .  +++..+..+|..++
T Consensus        81 ~--Y~I~i~~~~W~~Ll   95 (126)
T PF12921_consen   81 K--YPIPIPKEFWRRLL   95 (126)
T ss_pred             H--cCCCCCHHHHHHHH
Confidence            7  45666667776654

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

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=97.54  E-value=0.00037  Score=44.85  Aligned_cols=57  Identities=14%  Similarity=0.108  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +++.+...|.+.|++++|...|+++.+.  .|+...+..+...+.+.|+.++  .+++.+.
T Consensus       251 ~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l  309 (389)
T PRK11788        251 VLPKLMECYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQL  309 (389)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4555555666666666666666655543  3444444555555555555555  4444443

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

Probab=97.42  E-value=0.0001  Score=52.46  Aligned_cols=50  Identities=12%  Similarity=0.179  Sum_probs=35.0

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcc
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK   54 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~   54 (87)
                      .||.+||.++|..||..|+++.|- +|..|......-+...|+.++.+...
T Consensus        22 ~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~   71 (1088)
T KOG4318|consen   22 LPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKE   71 (1088)
T ss_pred             CCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccc
Confidence            588899999999999999999998 88887654333333333333333333

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=97.42  E-value=0.0006  Score=43.89  Aligned_cols=70  Identities=13%  Similarity=-0.032  Sum_probs=55.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcc---cchhHH--HHHHhchhcccccccchhh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK---IKIFGV--TLMGIQPQNLWYYIDGQID   79 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~---~~~~~~--~~~~~m~~~~~~g~~~~~~   79 (87)
                      |+...++.+...+.+.|++++|..+|.++.+.  .||..++..++.....   .|..++  .+++.+.++   ++.|+..
T Consensus       280 p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~---~~~~~p~  354 (389)
T PRK11788        280 PGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGE---QLKRKPR  354 (389)
T ss_pred             CCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHH---HHhCCCC
Confidence            55566789999999999999999999998765  6999999999988775   335555  788888876   5655544

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

Probab=97.09  E-value=0.0015  Score=43.47  Aligned_cols=51  Identities=16%  Similarity=0.037  Sum_probs=46.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHccc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKI   55 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~   55 (87)
                      ||..|+|.||+.+.++|++..|.++..+|...+...+..|+..-+.+|.+.
T Consensus       136 ~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  136 PDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             CChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            789999999999999999999999999999888888888998888888776

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 [].

>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=96.97  E-value=0.0047  Score=30.16  Aligned_cols=51  Identities=20%  Similarity=0.218  Sum_probs=41.5

Q ss_pred             HhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           18 AKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        18 ~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+.|++++|+++|++.....-. |......+..++.+.|++++  .+++.+...
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPD-NPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTT-SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hhccCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5689999999999999876422 66677789999999999999  888888765

...

>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=96.92  E-value=0.0089  Score=33.67  Aligned_cols=71  Identities=7%  Similarity=-0.041  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc--ccccccchhhh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN--LWYYIDGQIDA   80 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~--~~~g~~~~~~~   80 (87)
                      ....++..+...|++++|..+.++..... .-|...|..+|.++...|+...  ++|+.+...  ...|+.|+..+
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            45667778888999999999999988664 3388899999999999999988  666555432  12588888765

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

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

Probab=96.64  E-value=0.0074  Score=43.52  Aligned_cols=73  Identities=14%  Similarity=0.094  Sum_probs=61.0

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAW   81 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~   81 (87)
                      .+|..+|.+++..-.-+|+.+-|..+..+|+++|+..+..-|=.+|-+   .+....  .+...|...   |+.|+..|+
T Consensus       201 ~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~---gv~p~seT~  274 (1088)
T KOG4318|consen  201 APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEK---GVQPGSETQ  274 (1088)
T ss_pred             CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHh---cCCCCcchh
Confidence            478899999999999999999999999999999998888866666665   444444  778888887   999999887


Q ss_pred             h
Q 042815           82 Q   82 (87)
Q Consensus        82 ~   82 (87)
                      .
T Consensus       275 a  275 (1088)
T KOG4318|consen  275 A  275 (1088)
T ss_pred             H
Confidence            4

>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=96.55  E-value=0.021  Score=31.98  Aligned_cols=56  Identities=11%  Similarity=-0.107  Sum_probs=48.9

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHH-HcCCCCCHhhHHHHHHHHcccchhH
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIE-KRGPRPNAVTFVGVLTAYGKIKIFG   59 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~-~~g~~pd~~t~~~ll~~~~~~~~~~   59 (87)
                      .|+...-.+++.+|+.+|++..|+++.+... ..++.-+..+|..|++-+-.....+
T Consensus        49 ~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~~~  105 (126)
T PF12921_consen   49 YPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSSKR  105 (126)
T ss_pred             CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCCc
Confidence            4899999999999999999999999999987 5688889999999999887655543

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

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

Probab=96.42  E-value=0.02  Score=36.79  Aligned_cols=79  Identities=10%  Similarity=0.064  Sum_probs=62.6

Q ss_pred             CCcHhHHHHHHHHHHhc-----CCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH------------------
Q 042815            4 PRDATTSSAMMLGLAKN-----GKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV------------------   60 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~-----g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~------------------   60 (87)
                      ++|-.+|-+++..|...     +++|=...-++.|.+.|+..|..+|..||..+-+...+..                  
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I  143 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAI  143 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHH
Confidence            57888999999988775     6677777788999999999999999999999887544322                  


Q ss_pred             HHHHhchhcccccccchhhhhhccc
Q 042815           61 TLMGIQPQNLWYYIDGQIDAWQAAC   85 (87)
Q Consensus        61 ~~~~~m~~~~~~g~~~~~~~~~~~~   85 (87)
                      .++++|...   |+-||..+--.++
T Consensus       144 ~vLeqME~h---GVmPdkE~e~~lv  165 (406)
T KOG3941|consen  144 KVLEQMEWH---GVMPDKEIEDILV  165 (406)
T ss_pred             HHHHHHHHc---CCCCchHHHHHHH
Confidence            567778776   9999887654444

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

Probab=96.39  E-value=0.019  Score=39.92  Aligned_cols=51  Identities=12%  Similarity=-0.004  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .+..+...|.+.|++++|...|+++.+.+.. |..++..+..++.+.|+.++
T Consensus       839 ~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~g~~~~  889 (899)
T TIGR02917       839 ILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLALALLATGRKAE  889 (899)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHHHcCCHHH
Confidence            3444444444455555555555555444322 44444445555555555444

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.

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

Probab=96.02  E-value=0.024  Score=24.47  Aligned_cols=26  Identities=8%  Similarity=0.050  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIE   34 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~   34 (87)
                      +|+.|=..|.+.|++++|+++|++..
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            57888899999999999999999954

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

Probab=95.88  E-value=0.06  Score=37.56  Aligned_cols=53  Identities=13%  Similarity=0.102  Sum_probs=24.6

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ...|..+...|.+.|++++|...|+++.+.. ..+...+..+..++...|+.++
T Consensus       601 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  653 (899)
T TIGR02917       601 PEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAK  653 (899)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHH
Confidence            3445555555555555555555555544332 1133344444444444444444

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.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.75  E-value=0.039  Score=24.85  Aligned_cols=28  Identities=11%  Similarity=-0.006  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      +|..+-..|.+.|++++|.++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5778888999999999999999999876

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

Probab=95.56  E-value=0.071  Score=25.69  Aligned_cols=53  Identities=11%  Similarity=0.071  Sum_probs=42.0

Q ss_pred             HHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           14 MLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        14 i~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      -..+.+.|++++|...|++.....  | +...+..+-.++...|+.++  ..|+....
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            356789999999999999998765  5 55577778888889999988  77777754

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

Probab=95.53  E-value=0.094  Score=35.90  Aligned_cols=58  Identities=10%  Similarity=0.138  Sum_probs=47.9

Q ss_pred             CCCCcHhHHHHHHHHHHh-cCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            2 MPPRDATTSSAMMLGLAK-NGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         2 m~~~~~~~~~~li~~~~~-~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      +-+|+.+-|..||..|.+ .|++.+|.++|+..- +.+.-|.-....+++-|...|.-+.
T Consensus       654 liqp~~~kwqlmiasc~rrsgnyqka~d~yk~~h-rkfpedldclkflvri~~dlgl~d~  712 (840)
T KOG2003|consen  654 LIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIH-RKFPEDLDCLKFLVRIAGDLGLKDA  712 (840)
T ss_pred             hcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHH-HhCccchHHHHHHHHHhccccchhH
Confidence            357999999999988765 799999999999974 4456688888999999998886554

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

Probab=95.52  E-value=0.038  Score=31.07  Aligned_cols=41  Identities=20%  Similarity=0.302  Sum_probs=30.0

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHH-----HcCCCCCHhhH
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIE-----KRGPRPNAVTF   45 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~-----~~g~~pd~~t~   45 (87)
                      -|...|-.+|.+|.+.|+..+|.+.|+++.     +.|+.|...+-
T Consensus        94 ~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   94 YDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            467789999999999999999999999975     35899987654

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

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=95.27  E-value=0.073  Score=23.05  Aligned_cols=29  Identities=14%  Similarity=0.176  Sum_probs=24.6

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      ..+++.|-..|...|++++|+.++++...
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            35788999999999999999999999763

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=95.04  E-value=0.23  Score=28.18  Aligned_cols=62  Identities=3%  Similarity=-0.131  Sum_probs=36.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+...|..+-..+.+.|++++|...|++..... ..|...+..+-.++...|+.++  ..|+...
T Consensus        56 ~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al  119 (144)
T PRK15359         56 WSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGEPGLAREAFQTAI  119 (144)
T ss_pred             CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            355566666666666667777777666665432 1244455555556666666666  5555544

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=94.69  E-value=0.099  Score=26.10  Aligned_cols=59  Identities=8%  Similarity=0.071  Sum_probs=42.8

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHc--CCC---CC-HhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKR--GPR---PN-AVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~--g~~---pd-~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      .+|+.+-..|...|++++|+..|++..+.  ...   |+ ..++..+=.++...|+.++  ..+++.
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            57888999999999999999999997743  122   23 4467777777788888877  555543

...

>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=94.65  E-value=0.23  Score=24.08  Aligned_cols=59  Identities=17%  Similarity=0.121  Sum_probs=45.7

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccc-hhHH--HHHHhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIK-IFGV--TLMGIQ   66 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~-~~~~--~~~~~m   66 (87)
                      +...|..+=..+.+.|++++|+..|.+..+..  | +...|..+=.++...| +.++  ..++..
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~--p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD--PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS--TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            45678888889999999999999999988764  4 5557777777788888 6665  555443

...

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

Probab=94.54  E-value=0.11  Score=25.08  Aligned_cols=42  Identities=17%  Similarity=0.255  Sum_probs=32.1

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVL   49 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll   49 (87)
                      |...+-.+...|.+.|++++|.+++.++...  .||...|..++
T Consensus        24 ~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen   24 NPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            6667778999999999999999999998866  46655554443

...

>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=94.31  E-value=0.28  Score=23.80  Aligned_cols=57  Identities=14%  Similarity=0.022  Sum_probs=29.4

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      |..+...+.+.|++++|..+|.+..+.. ..+...+..+-..+...++.+.  ..++...
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~   61 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKAL   61 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555666666666666666655432 1122344444555555555555  4444433

>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=94.19  E-value=0.1  Score=29.70  Aligned_cols=33  Identities=18%  Similarity=0.324  Sum_probs=26.1

Q ss_pred             hcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHc
Q 042815           19 KNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYG   53 (87)
Q Consensus        19 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~   53 (87)
                      +.|.-.+|..+|.+|...|-.||.  |+.|+..+.
T Consensus       107 ~ygsk~DaY~VF~kML~~G~pPdd--W~~Ll~~a~  139 (140)
T PF11663_consen  107 AYGSKTDAYAVFRKMLERGNPPDD--WDALLKEAK  139 (140)
T ss_pred             hhccCCcHHHHHHHHHhCCCCCcc--HHHHHHHhc
Confidence            446678999999999999999984  666776653

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 [].

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

Probab=94.18  E-value=0.28  Score=30.50  Aligned_cols=61  Identities=7%  Similarity=-0.093  Sum_probs=34.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .|...|..+-..+.+.|+.++|++.|++....  .| |......++..+...|+.++  .++....
T Consensus       144 ~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~  207 (280)
T PF13429_consen  144 DSARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLL  207 (280)
T ss_dssp             T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            34555666666666666666676666666544  34 34455566666666666654  4444443

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

Probab=93.99  E-value=0.26  Score=31.92  Aligned_cols=57  Identities=14%  Similarity=0.208  Sum_probs=46.3

Q ss_pred             CCcHhHHHHHHHHHHhcC----------------CchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            4 PRDATTSSAMMLGLAKNG----------------KNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g----------------~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ++|..+|+.||.-+-+-.                +-+=++.++++|...|+.||..+--.|+.++++-+..-.
T Consensus       104 erDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~  176 (406)
T KOG3941|consen  104 ERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTK  176 (406)
T ss_pred             hhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccHH
Confidence            478889999888766532                124478899999999999999999999999999886544

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.64  E-value=0.65  Score=31.55  Aligned_cols=62  Identities=11%  Similarity=0.077  Sum_probs=50.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCH----hhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNA----VTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~----~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|+.+-.+|.+.|++++|+..|++-.+.  .||.    .+|..+-.+|+..|++++  ..+.+...
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45678999999999999999999999996654  5664    469999999999999988  55555443

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

Probab=93.53  E-value=0.45  Score=26.03  Aligned_cols=60  Identities=13%  Similarity=0.210  Sum_probs=33.8

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ......+...+.+.|++++|.+.|++....+ ..+...+..+-..+...|+.+.  ..++...
T Consensus        17 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~   78 (135)
T TIGR02552        17 LEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAA   78 (135)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455556666677777777776665443 2244455555555556666655  4555443

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

>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=93.52  E-value=0.43  Score=23.11  Aligned_cols=61  Identities=16%  Similarity=0.085  Sum_probs=45.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|...|++++|.+.|.+..... ..+..++..+...+...|+.+.  ..+....
T Consensus        33 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~   95 (100)
T cd00189          33 NADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGKYEEALEAYEKAL   95 (100)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            34677888888999999999999999977654 2244577777777888888776  5555443

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=93.29  E-value=0.26  Score=31.67  Aligned_cols=42  Identities=17%  Similarity=0.243  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLT   50 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~   50 (87)
                      =||.-|..-.+.|++++|+.|.+|-+..|+.--..||...++
T Consensus       259 Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V~  300 (303)
T PRK10564        259 YFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSVK  300 (303)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHhh
Confidence            467999999999999999999999999998877777755443

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

Probab=93.19  E-value=0.77  Score=29.32  Aligned_cols=73  Identities=10%  Similarity=0.005  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc--ccccccchhhhhh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN--LWYYIDGQIDAWQ   82 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~--~~~g~~~~~~~~~   82 (87)
                      ++..++..+...|+++.+.+.+++..... .-|...|..++.++.+.|....  ..|+++...  -..|++|...+..
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~  231 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRA  231 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHH
Confidence            45556666666666777777666666553 2266667777777777666655  444443321  1146666655543

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

Probab=93.09  E-value=0.8  Score=25.01  Aligned_cols=64  Identities=0%  Similarity=-0.108  Sum_probs=49.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|...|++....+ ..+...+..+-..+...|+.+.  ..|......
T Consensus        49 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        49 YNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            466788888899999999999999999976654 3355667667778888899887  777766543

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

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

Probab=92.94  E-value=0.13  Score=26.14  Aligned_cols=52  Identities=15%  Similarity=0.093  Sum_probs=27.4

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ...|-.+-..|.+.|++++|..++++ ...+-. +....-.+-.++-+.|+.++
T Consensus        25 ~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~-~~~~~~l~a~~~~~l~~y~e   76 (84)
T PF12895_consen   25 SAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPS-NPDIHYLLARCLLKLGKYEE   76 (84)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHC-HHHHHHHHHHHHHHTT-HHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCC-CHHHHHHHHHHHHHhCCHHH
Confidence            33444467777777777777777776 222111 11222233455566666665

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

Probab=92.88  E-value=0.81  Score=29.21  Aligned_cols=51  Identities=16%  Similarity=0.196  Sum_probs=43.5

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHH-----cCCCCCHhhHHHHHHHHcc
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEK-----RGPRPNAVTFVGVLTAYGK   54 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~g~~pd~~t~~~ll~~~~~   54 (87)
                      +-|...|-.+|.+|.++|+...|+..|+++..     .|+.|-..+.....+...+
T Consensus       184 p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~~~~~~  239 (280)
T COG3629         184 PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYEEILRQ  239 (280)
T ss_pred             ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhcc
Confidence            45778899999999999999999999999875     5899998888877777444

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B

Probab=92.82  E-value=0.21  Score=24.47  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=20.5

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHH
Q 042815           12 AMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus        12 ~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      .+|.||.+.|++++|.+...++..
T Consensus        28 qvI~gllqlg~~~~a~eYi~~~~~   51 (62)
T PF14689_consen   28 QVIYGLLQLGKYEEAKEYIKELSK   51 (62)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            579999999999999999988763

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

Probab=92.58  E-value=0.38  Score=19.93  Aligned_cols=29  Identities=7%  Similarity=-0.026  Sum_probs=24.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      .+|..+-..|...|++++|+..|++..+.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            46888889999999999999999997754

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 ....

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

Probab=92.56  E-value=0.42  Score=30.17  Aligned_cols=62  Identities=6%  Similarity=-0.055  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcC-CCCCHhhHHHHHHHHcccchhHH-HHHHhchhc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRG-PRPNAVTFVGVLTAYGKIKIFGV-TLMGIQPQN   69 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t~~~ll~~~~~~~~~~~-~~~~~m~~~   69 (87)
                      .+|-.++...-+.+..+.|..+|.+..+.+ +..+.+...+.++-++....-.. .+|+...+.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~   65 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK   65 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            467788888888888888888888887543 55677777777766644332223 777777765

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=92.51  E-value=1.2  Score=25.78  Aligned_cols=61  Identities=10%  Similarity=-0.003  Sum_probs=42.5

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ...|..+-..|.+.|++++|...|.+..... ..+...+..+...+...|+.+.  ..++....
T Consensus       135 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  197 (234)
T TIGR02521       135 ARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQ  197 (234)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3456667777888888888888888876543 1234567777777778888877  66665544

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=92.35  E-value=1.3  Score=25.67  Aligned_cols=24  Identities=17%  Similarity=0.070  Sum_probs=9.6

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHH
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSI   33 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m   33 (87)
                      |..+...|.+.|++++|.+.|++.
T Consensus        68 ~~~la~~~~~~~~~~~A~~~~~~a   91 (234)
T TIGR02521        68 YLALALYYQQLGELEKAEDSFRRA   91 (234)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            333333344444444444444433

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.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=92.32  E-value=0.5  Score=25.53  Aligned_cols=46  Identities=9%  Similarity=0.022  Sum_probs=37.6

Q ss_pred             hhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           24 GMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        24 ~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      =+..+-++.+....+.|+.....+.|+||-+..++..  ++++..+.+
T Consensus        24 we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K   71 (103)
T cd00923          24 WELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK   71 (103)
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            3455566677777899999999999999999999888  888888755

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.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=92.16  E-value=0.98  Score=23.76  Aligned_cols=60  Identities=10%  Similarity=0.089  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCC-C-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPR-P-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+..+-..+.+.|++++|...|++.....-. | ...++..+-.++.+.++.+.  ..+.....
T Consensus        41 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  104 (119)
T TIGR02795        41 AHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIK  104 (119)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHH
Confidence            3444556666667777777777666543211 1 12234444445555555555  55555544

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

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=91.83  E-value=0.83  Score=22.23  Aligned_cols=54  Identities=4%  Similarity=-0.054  Sum_probs=41.3

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ..|.+.+++++|.+.++++....- .+...+...=.++.+.|++..  ..++.....
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDP-DDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCc-ccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            467899999999999999987642 255566666777888888888  777777654

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

Probab=91.81  E-value=0.41  Score=26.10  Aligned_cols=45  Identities=9%  Similarity=0.020  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           25 MGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        25 ~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +..+-++.+-...+.|+.....+.|+||-+..++..  ++++..+.+
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            444555666677889999999999999999999888  888888876

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 ....

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

Probab=91.42  E-value=0.93  Score=28.19  Aligned_cols=65  Identities=11%  Similarity=-0.000  Sum_probs=41.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcC-CCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRG-PRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ++...+..++..|.+.|+++++.+++.+..... ..++...|...-..+.+.|+.++  ..+++....
T Consensus       108 ~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~  175 (280)
T PF13429_consen  108 GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALEL  175 (280)
T ss_dssp             ----------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_pred             cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            455677888899999999999999999977433 45577788888888899999988  788777654

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.39  E-value=0.21  Score=21.26  Aligned_cols=25  Identities=12%  Similarity=0.178  Sum_probs=21.3

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHH
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVE   28 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~   28 (87)
                      +-|..+|+.+=..|.+.|++++|++
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEEAIA   34 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHhhcC
Confidence            4578899999999999999999863

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=90.90  E-value=0.65  Score=21.21  Aligned_cols=25  Identities=16%  Similarity=0.179  Sum_probs=21.9

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHHcC
Q 042815           13 MMLGLAKNGKNGMGVELFMSIEKRG   37 (87)
Q Consensus        13 li~~~~~~g~~~~a~~l~~~m~~~g   37 (87)
                      +-.+|...|+.+.|.+++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5578999999999999999998655

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=90.87  E-value=0.31  Score=19.81  Aligned_cols=24  Identities=25%  Similarity=0.289  Sum_probs=19.5

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHHc
Q 042815           13 MMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus        13 li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      +-..|.+.|++++|.+.|+++...
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHH
Confidence            345577889999999999998765

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=90.79  E-value=1.1  Score=25.84  Aligned_cols=52  Identities=12%  Similarity=0.099  Sum_probs=41.2

Q ss_pred             CcHhHHHHHHHHHHhcCC-chhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccc
Q 042815            5 RDATTSSAMMLGLAKNGK-NGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIK   56 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~-~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~   56 (87)
                      .|-.+|++++.+.++..- ---+..+|.-|++.+.++...-|..+|++|.+--
T Consensus        77 ~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g~  129 (145)
T PF13762_consen   77 LDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRGY  129 (145)
T ss_pred             cccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC
Confidence            455688899998877766 4556778888888888888889999999887763

>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=90.76  E-value=1.7  Score=23.72  Aligned_cols=28  Identities=11%  Similarity=0.121  Sum_probs=25.7

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      .-|..++.-|..+|..++|++++.+...
T Consensus        40 ~~~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen   40 GKYQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             CCHHHHHHHHHccCccHHHHHHHHHHhc
Confidence            4588999999999999999999999876

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.

>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2

Probab=90.53  E-value=1.2  Score=22.29  Aligned_cols=43  Identities=14%  Similarity=0.068  Sum_probs=36.1

Q ss_pred             HhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815           18 AKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus        18 ~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ...|+.+++.+++++....|..|.......+..+.-+.|..-.
T Consensus        12 l~~~d~~~~~~~~~~~l~~g~~~~~i~~~~l~p~m~~iG~~w~   54 (79)
T PF02607_consen   12 LLAGDEEEAEALLEEALAQGYPPEDIIEEILMPAMEEIGELWE   54 (79)
T ss_dssp             HHTT-CCHHHHHHHHHHHCSSSTTHHHHHTHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            3469999999999999989999999999889999888887643

1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=90.47  E-value=1  Score=20.81  Aligned_cols=37  Identities=16%  Similarity=0.106  Sum_probs=29.5

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHH
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTA   51 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~   51 (87)
                      ..--+.|...++..++++|.+.|+.-+...+..+++-
T Consensus        10 ~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen   10 LLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            3345778888999999999999988888877777653

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=90.28  E-value=2.3  Score=24.58  Aligned_cols=63  Identities=11%  Similarity=0.035  Sum_probs=44.5

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC--HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN--AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd--~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ....|..+-..|.+.|++++|...|++.....-.|+  ...+..+-..+.+.|+.+.  ..+.....
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  100 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE  100 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345667777778889999999999998876543332  3567777777888888877  55555443

>TIGR00540 hemY_coli hemY protein

Probab=90.23  E-value=2.5  Score=28.02  Aligned_cols=58  Identities=12%  Similarity=0.026  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      ...++=.-+.+.|++++|.+.|+........||..++..+-..+-+.|+.++  +++.+-
T Consensus       337 ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       337 INRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3446666678899999999999965555557898888899999999998877  666653

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.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=90.02  E-value=2.2  Score=24.07  Aligned_cols=58  Identities=10%  Similarity=-0.015  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...-..+.+.|++++|...|++..... ..+...+..+-.++...|+.++  ..|+....
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~   86 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALM   86 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            4456677889999999999999987553 2366688888888999999988  77777664

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.91  E-value=1  Score=29.65  Aligned_cols=42  Identities=12%  Similarity=0.105  Sum_probs=36.1

Q ss_pred             hcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815           19 KNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus        19 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      -.-++++++-+...=.+.|+-||.+|++.+|+.+-+.++..+
T Consensus       112 lky~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~  153 (418)
T KOG4570|consen  112 LKYDPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKD  153 (418)
T ss_pred             HccChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHH
Confidence            345678888888887899999999999999999999988776

>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=89.85  E-value=2.3  Score=29.62  Aligned_cols=23  Identities=4%  Similarity=-0.224  Sum_probs=9.2

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHH
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMS   32 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~   32 (87)
                      |..+-..|...|++++|...|++
T Consensus       402 ~~~lg~~~~~~g~~~~A~~~~~k  424 (615)
T TIGR00990       402 YYHRAQLHFIKGEFAQAGKDYQK  424 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            33333333444444444444443

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

Probab=89.79  E-value=3.1  Score=27.24  Aligned_cols=62  Identities=15%  Similarity=0.009  Sum_probs=46.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+-..|.+.|++++|+..+++....  .| +...|..+-.+|...|+++.  ..|+....
T Consensus        34 ~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--~P~~~~a~~~lg~~~~~lg~~~eA~~~~~~al~   98 (356)
T PLN03088         34 NNAELYADRAQANIKLGNFTEAVADANKAIEL--DPSLAKAYLRKGTACMKLEEYQTAKAALEKGAS   98 (356)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            35667778888888999999999999988765  34 45567777778888888877  66655543

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

Probab=89.64  E-value=0.71  Score=23.37  Aligned_cols=46  Identities=13%  Similarity=0.268  Sum_probs=35.1

Q ss_pred             cCCchhHHHHHHHHHHcCC-CCCHhhHHHHHHHHcccchhHH--HHHHh
Q 042815           20 NGKNGMGVELFMSIEKRGP-RPNAVTFVGVLTAYGKIKIFGV--TLMGI   65 (87)
Q Consensus        20 ~g~~~~a~~l~~~m~~~g~-~pd~~t~~~ll~~~~~~~~~~~--~~~~~   65 (87)
                      .|++++|+.+|+++.+..- .|+...+-.+-.++.+.|+.+.  .++..
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            6899999999999987653 2345555557889999999988  77776

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=89.48  E-value=0.79  Score=18.09  Aligned_cols=22  Identities=18%  Similarity=0.172  Sum_probs=17.5

Q ss_pred             HHHHHHHHhcCCchhHHHHHHH
Q 042815           11 SAMMLGLAKNGKNGMGVELFMS   32 (87)
Q Consensus        11 ~~li~~~~~~g~~~~a~~l~~~   32 (87)
                      ..+-..+...|++++|..++++
T Consensus         5 ~~la~~~~~~G~~~eA~~~l~~   26 (26)
T PF07721_consen    5 LALARALLAQGDPDEAERLLRR   26 (26)
T ss_pred             HHHHHHHHHcCCHHHHHHHHhC
Confidence            4556778899999999998763

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

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

Probab=88.89  E-value=1.5  Score=30.34  Aligned_cols=60  Identities=8%  Similarity=0.103  Sum_probs=50.1

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcC-CCCCHhhHHHHHHHHcccchhHH-HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRG-PRPNAVTFVGVLTAYGKIKIFGV-TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t~~~ll~~~~~~~~~~~-~~~~~m~   67 (87)
                      .+|-..|..-.+..-++.|..+|-+..+.| +.|+++.++++|.-++.....-. ++|+.=.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d~~ta~~ifelGl  459 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGDRATAYNIFELGL  459 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCCcchHHHHHHHHH
Confidence            567788888888888999999999999999 77899999999999998766655 7776433

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

Probab=88.87  E-value=1.6  Score=20.75  Aligned_cols=31  Identities=6%  Similarity=0.000  Sum_probs=26.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      +.-.|..+-..+.+.|++++|...|++..+.
T Consensus        30 ~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen   30 NPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6677888888999999999999999998754

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=88.71  E-value=4.4  Score=26.83  Aligned_cols=58  Identities=17%  Similarity=0.099  Sum_probs=40.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGI   65 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~   65 (87)
                      |.....++=..+.+.|++++|.+.|++..+.  .|+..++..+-..+.+.|+.++  ..+.+
T Consensus       327 ~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~  386 (398)
T PRK10747        327 TPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRD  386 (398)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            3344556666777788888888888876654  5777777777777777777766  44443

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

Probab=88.33  E-value=1.1  Score=18.23  Aligned_cols=28  Identities=11%  Similarity=-0.014  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      .|..+=..|.+.|++++|++.|++....
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l   30 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4566667889999999999999997654

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=88.17  E-value=2.6  Score=24.88  Aligned_cols=53  Identities=8%  Similarity=-0.002  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh--hHHHHHHHHcccchhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV--TFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~--t~~~ll~~~~~~~~~~~   60 (87)
                      ..+..+-.-|++.|+.++|++.|.++.+....|...  .+-.+|+.+-..+++..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~   91 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSH   91 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHH
Confidence            467788899999999999999999998876666544  55667777777777665

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.

>PRK12370 invasion protein regulator; Provisional

Probab=88.15  E-value=4.8  Score=27.90  Aligned_cols=27  Identities=11%  Similarity=-0.063  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      .|..+-..|...|++++|...|++..+
T Consensus       374 a~~~lg~~l~~~G~~~eAi~~~~~Al~  400 (553)
T PRK12370        374 IKYYYGWNLFMAGQLEEALQTINECLK  400 (553)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            444444455555555555555555443

>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=87.99  E-value=2.8  Score=26.77  Aligned_cols=53  Identities=9%  Similarity=0.077  Sum_probs=25.9

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIF   58 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~   58 (87)
                      ++..+.|.+..++...|++++|.+++.+.....- -|..|...++.+....|+.
T Consensus       199 ~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-~~~d~LaNliv~~~~~gk~  251 (290)
T PF04733_consen  199 STPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-NDPDTLANLIVCSLHLGKP  251 (290)
T ss_dssp             -SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHTT-T
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCC
Confidence            3445555666666666666666666665443221 1333555555555555554

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.

>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=87.52  E-value=5  Score=26.96  Aligned_cols=60  Identities=15%  Similarity=0.137  Sum_probs=45.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh-hHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV-TFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      |....+.-...+.+.++++.|+.+.++....  .|+.. +|..|..+|.+.|+++.  ..++.+.
T Consensus       233 d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  233 DSELLNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            4444555556678889999999999997755  67666 99999999999999988  5555444

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

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=87.50  E-value=1.6  Score=25.88  Aligned_cols=32  Identities=16%  Similarity=0.133  Sum_probs=28.1

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      .|+...|..++..+...|+.++|.+..+++..
T Consensus       141 ~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~  172 (193)
T PF11846_consen  141 RPDPNVYQRYALALALLGDPEEARQWLARARR  172 (193)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            47888899999999999999999999988763

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>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=87.30  E-value=3.6  Score=23.85  Aligned_cols=62  Identities=18%  Similarity=0.153  Sum_probs=42.5

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhccccccc
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYID   75 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~   75 (87)
                      .+.-+....+.|+-++-.++++++.+.+ +|+.....-+-.||.+.|..++  +++....++   |+.
T Consensus        89 vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACek---G~k  152 (161)
T PF09205_consen   89 VDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEK---GLK  152 (161)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHT---T-H
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHh---chH
Confidence            3445666777888888888888876543 7888888899999999999988  888877776   664

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=87.24  E-value=6.2  Score=28.05  Aligned_cols=61  Identities=10%  Similarity=0.095  Sum_probs=35.1

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC-HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN-AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...+..+-..+.+.|++++|...|++....  .|+ ...+..+-.++.+.|+.++  ..+..+..
T Consensus       283 ~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l--~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~  346 (656)
T PRK15174        283 NVRIVTLYADALIRTGQNEKAIPLLQQSLAT--HPDLPYVRAMYARALRQVGQYTAASDEFVQLAR  346 (656)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4456666666666666666666666665543  233 3344455555666666665  55555443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=87.16  E-value=4  Score=23.40  Aligned_cols=61  Identities=7%  Similarity=-0.104  Sum_probs=43.2

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC--HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN--AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd--~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...|..+...+...|++++|+..|++.....-.|.  ..++..+=..+...|+.++  ..++...
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al   99 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQAL   99 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45677777788888999999999998865532222  2467777777778888877  5555544

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

Probab=87.04  E-value=3.3  Score=29.19  Aligned_cols=62  Identities=11%  Similarity=-0.015  Sum_probs=46.0

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh-hHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV-TFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      -|+.+|+.||.-+ +...++++.+.++++.  +..|... .|..-|++--...+++.  .+|.+-..+
T Consensus        18 ~di~sw~~lire~-qt~~~~~~R~~YEq~~--~~FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvk   82 (656)
T KOG1914|consen   18 YDIDSWSQLIREA-QTQPIDKVRETYEQLV--NVFPSSPRAWKLYIERELASKDFESVEKLFSRCLVK   82 (656)
T ss_pred             ccHHHHHHHHHHH-ccCCHHHHHHHHHHHh--ccCCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            3888999999955 4449999999999986  4456544 67777777777777777  777766544

>PRK11189 lipoprotein NlpI; Provisional

Probab=86.74  E-value=6.1  Score=25.07  Aligned_cols=53  Identities=15%  Similarity=0.086  Sum_probs=30.5

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC-HhhHHHHHHHHcccchhHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN-AVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~~~~~~~~~~~   60 (87)
                      +...|+.+=..|.+.|++++|.+.|++..+.  .|+ ..+|..+-.++...|+.++
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~e  150 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIALYYGGRYEL  150 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHH
Confidence            4556666666666677777777766665533  342 3344444444555555555

>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP)

Probab=86.67  E-value=0.17  Score=24.33  Aligned_cols=35  Identities=17%  Similarity=0.287  Sum_probs=30.0

Q ss_pred             CCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHccc
Q 042815           21 GKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKI   55 (87)
Q Consensus        21 g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~   55 (87)
                      |--++..++|++|+.+...|.+-.|+..|+-|...
T Consensus         6 gy~~~lI~vFK~~pSr~YD~~Tr~W~F~L~Dy~~L   40 (55)
T PF07443_consen    6 GYHEELIAVFKQMPSRNYDPKTRKWNFSLEDYSTL   40 (55)
T ss_pred             cCCHHHHHHHHcCcccccCccceeeeeeHHHHHHH
Confidence            55578899999999999999999999888877654

This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=86.47  E-value=4  Score=22.67  Aligned_cols=53  Identities=8%  Similarity=0.136  Sum_probs=32.9

Q ss_pred             HHHhcCCchhHHHHHHHHHHcCCCCCH--hhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           16 GLAKNGKNGMGVELFMSIEKRGPRPNA--VTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        16 ~~~~~g~~~~a~~l~~~m~~~g~~pd~--~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ++-..|+.++|+.+|++-...|.....  ..+..+-+.+-..|++++  .+++....
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345567777777777777777755442  244455556666777776  55555544

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=85.92  E-value=1.6  Score=17.77  Aligned_cols=27  Identities=11%  Similarity=-0.007  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      +|..+=..|.+.|++++|...|++-.+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            566677788999999999999998654

...

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=85.80  E-value=5.7  Score=27.67  Aligned_cols=68  Identities=13%  Similarity=0.070  Sum_probs=45.1

Q ss_pred             HHHhcCCchhHHHHHHHHHHcC-CCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhhccc
Q 042815           16 GLAKNGKNGMGVELFMSIEKRG-PRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQAAC   85 (87)
Q Consensus        16 ~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~~~~   85 (87)
                      ..-+.|+.++|.+.|++|.+.- ..-+......|++++-..+...+  .++.+....  ..-..-...||+++
T Consensus       268 CarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi--~lpkSAti~YTaAL  338 (539)
T PF04184_consen  268 CARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDI--SLPKSATICYTAAL  338 (539)
T ss_pred             HHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccc--cCCchHHHHHHHHH
Confidence            3345699999999999998553 22345578889999999988877  666655432  11123334566553

The molecular function of this protein is uncertain.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=85.67  E-value=3.6  Score=21.49  Aligned_cols=59  Identities=14%  Similarity=0.057  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC----HhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN----AVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ++-.....+.+.|++++|...|.++....  |+    ...+..+-..+.+.|+.+.  ..++.....
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~   68 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKY--PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKK   68 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence            45566777899999999999999997652  33    2355567788888899887  777776653

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=85.67  E-value=6.9  Score=25.22  Aligned_cols=48  Identities=4%  Similarity=0.108  Sum_probs=34.6

Q ss_pred             chhHHHHHHHHHHcCCCCCHhhHHHHHHHHcc--cchhHH------HHHHhchhcc
Q 042815           23 NGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK--IKIFGV------TLMGIQPQNL   70 (87)
Q Consensus        23 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~--~~~~~~------~~~~~m~~~~   70 (87)
                      +++.+.+++.|.+.|++-+..+|.+.+--...  ....+.      .+|..|+++|
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H  133 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKH  133 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhC
Confidence            46677799999999999999988774333333  333333      8999999883

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

Probab=85.15  E-value=2.9  Score=27.66  Aligned_cols=63  Identities=10%  Similarity=0.055  Sum_probs=42.3

Q ss_pred             HHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhh
Q 042815           17 LAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDA   80 (87)
Q Consensus        17 ~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~   80 (87)
                      +...|++++|.+.++...+.+..--..+...+..+|...|+...  ..+.++... ..|..+-...
T Consensus       224 ~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~-~~g~~~~l~l  288 (389)
T COG2956         224 ELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET-NTGADAELML  288 (389)
T ss_pred             HHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-cCCccHHHHH
Confidence            55678899999998888877655555677788889999998887  333333322 1344444433

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

Probab=85.03  E-value=4.5  Score=28.51  Aligned_cols=68  Identities=9%  Similarity=-0.051  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQ   82 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~   82 (87)
                      +|+-|=-.|.+.+.+++|+..|++-.... .-|..|+.++=-.+...|.++.  ..||...     .+.|+..+-+
T Consensus       457 ~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL-----~l~p~n~~~~  526 (611)
T KOG1173|consen  457 TLNNLGHAYRKLNKYEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKAL-----ALKPDNIFIS  526 (611)
T ss_pred             HHHhHHHHHHHHhhHHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHH-----hcCCccHHHH
Confidence            45555566777788888888887765443 2366677777777777777777  6666554     3456554433

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

Probab=84.89  E-value=4.7  Score=24.16  Aligned_cols=64  Identities=8%  Similarity=-0.053  Sum_probs=48.0

Q ss_pred             CcHhHHHHHHHH-HHhcCC--chhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLG-LAKNGK--NGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~-~~~~g~--~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .|...|..+-.. |.+.|+  .++|.+++++..+..-. +...+..+-..+.+.|++++  ..|+.+...
T Consensus       105 ~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        105 ENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             CCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            466677777665 467777  59999999998866432 56677777778888999988  888887764

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

Probab=84.76  E-value=2.1  Score=30.75  Aligned_cols=48  Identities=8%  Similarity=0.083  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKI   57 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~   57 (87)
                      ..|++|-+-|.+.|++++|..+|.+-...  .-...-|+.++++|+....
T Consensus       249 ~Lw~SLAdYYIr~g~~ekarDvyeeai~~--v~tvrDFt~ifd~Ya~FEE  296 (835)
T KOG2047|consen  249 FLWCSLADYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIFDAYAQFEE  296 (835)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHHHHHHHHHH
Confidence            57999999999999999999999996644  3355567888888876543

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=84.51  E-value=4.6  Score=21.72  Aligned_cols=49  Identities=16%  Similarity=0.217  Sum_probs=39.5

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815           12 AMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus        12 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .++..+...+..-.|.++++++.+.+..++..|.--.|+.+.+.|.+..
T Consensus         5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~   53 (116)
T cd07153           5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE   53 (116)
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence            3566666667778899999999998877888888888888888887765

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

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

Probab=84.37  E-value=8.2  Score=24.48  Aligned_cols=54  Identities=15%  Similarity=0.108  Sum_probs=39.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      |...-+..+....++|++++|...|++...- -.+|...|+-+=-+|.+.|+++.
T Consensus        99 d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~Gr~~~  152 (257)
T COG5010          99 DRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLGRFDE  152 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHccChhH
Confidence            3334455677777888888888888886533 25677788888888888888887

>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]

Probab=83.94  E-value=4.8  Score=21.50  Aligned_cols=57  Identities=11%  Similarity=0.037  Sum_probs=32.8

Q ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchh-HH---HHHHhchhc
Q 042815           11 SAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIF-GV---TLMGIQPQN   69 (87)
Q Consensus        11 ~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~-~~---~~~~~m~~~   69 (87)
                      +.+|..|..+|+.++|...+.++.....  .......++..+...+.- .+   .++..+...
T Consensus         6 ~~~l~ey~~~~d~~ea~~~l~el~~~~~--~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~   66 (113)
T PF02847_consen    6 FSILMEYFSSGDVDEAVECLKELKLPSQ--HHEVVKVILECALEEKKSYREYYSKLLSHLCKR   66 (113)
T ss_dssp             HHHHHHHHHHT-HHHHHHHHHHTT-GGG--HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHhCCCcc--HHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhc
Confidence            5677889999999999999988753311  122333344444444232 22   666666554

It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....

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

Probab=83.88  E-value=0.94  Score=33.49  Aligned_cols=64  Identities=8%  Similarity=0.175  Sum_probs=49.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +|..+=|-+=.-++.+|++++|..+|.+..+... -+.-+|..+-++|...|++..  +.|+.-.++
T Consensus       644 kN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  644 KNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             chhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555565667889999999999999987754 245577888889999999888  778777765

>PRK12370 invasion protein regulator; Provisional

Probab=83.82  E-value=12  Score=25.98  Aligned_cols=56  Identities=4%  Similarity=-0.139  Sum_probs=36.5

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHHcCCCCCH-hhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           12 AMMLGLAKNGKNGMGVELFMSIEKRGPRPNA-VTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        12 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~-~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...+...|++++|...+++..... .|+. ..+..+-.++...|+.++  ..+..+..
T Consensus       411 ~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~  469 (553)
T PRK12370        411 TKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEIST  469 (553)
T ss_pred             HHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhh
Confidence            34445666888999999998876543 3433 345555666777888887  66665543

>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=83.66  E-value=10  Score=26.50  Aligned_cols=51  Identities=10%  Similarity=-0.157  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      +|..+-..|...|++++|...|++..+.. .-+...|..+-..+...|+.++
T Consensus       367 ~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~  417 (615)
T TIGR00990       367 SYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQ  417 (615)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHH
Confidence            44445555555555555555555554331 1123344444445555555554

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=83.56  E-value=13  Score=25.96  Aligned_cols=60  Identities=7%  Similarity=-0.093  Sum_probs=47.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|.++-......|++++|...|++.....  |+...|..+-+.+...|+.++  ..+.+..
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~  480 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAF  480 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34567777555667899999999999988765  788899999999999999988  6665554

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

Probab=83.38  E-value=4.9  Score=28.34  Aligned_cols=52  Identities=15%  Similarity=0.206  Sum_probs=43.8

Q ss_pred             CCCCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHccc
Q 042815            2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKI   55 (87)
Q Consensus         2 m~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~   55 (87)
                      +.+.|..+++++=--|...|+++.|.+.|++  ...+.||-.+-+.+|..+-..
T Consensus       484 l~~k~~~~~asig~iy~llgnld~Aid~fhK--aL~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  484 LSPKDASTHASIGYIYHLLGNLDKAIDHFHK--ALALKPDNIFISELLKLAIED  535 (611)
T ss_pred             cCCCchhHHHHHHHHHHHhcChHHHHHHHHH--HHhcCCccHHHHHHHHHHHHh
Confidence            4567888999998899999999999999999  557799998888888866544

>COG4003 Uncharacterized protein conserved in archaea [Function unknown]

Probab=83.17  E-value=1.8  Score=22.75  Aligned_cols=39  Identities=23%  Similarity=0.290  Sum_probs=28.3

Q ss_pred             CCCCcHhHHH-HHHHHHHhcCCchhHHHHHHHHHHcC-CCC
Q 042815            2 MPPRDATTSS-AMMLGLAKNGKNGMGVELFMSIEKRG-PRP   40 (87)
Q Consensus         2 m~~~~~~~~~-~li~~~~~~g~~~~a~~l~~~m~~~g-~~p   40 (87)
                      ||+-|..-|| ++++-+.++.-.++|+++.+-|.+.| +.|
T Consensus        25 ~~~~~~~gy~PtV~D~L~rCdT~EEAlEii~yleKrGEi~~   65 (98)
T COG4003          25 EPKIDFSGYNPTVIDFLRRCDTEEEALEIINYLEKRGEITP   65 (98)
T ss_pred             cccCCcCCCCchHHHHHHHhCcHHHHHHHHHHHHHhCCCCH
Confidence            3444444554 57777888888899999999999887 444

>smart00028 TPR Tetratricopeptide repeats

Probab=83.07  E-value=1.9  Score=16.15  Aligned_cols=27  Identities=11%  Similarity=0.035  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      .|..+-..|...|++++|...|.+..+
T Consensus         3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~   29 (34)
T smart00028        3 ALYNLGNAYLKLGDYDEALEYYEKALE   29 (34)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            567777888999999999999988653

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=82.99  E-value=9.2  Score=27.23  Aligned_cols=26  Identities=12%  Similarity=-0.040  Sum_probs=12.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSI   33 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m   33 (87)
                      ..|..+...+.+.|++++|...++++
T Consensus       145 ~a~~~la~~l~~~g~~~eA~~~~~~~  170 (656)
T PRK15174        145 QIFALHLRTLVLMDKELQAISLARTQ  170 (656)
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHH
Confidence            34444444444444444444444444

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

Probab=82.83  E-value=10  Score=26.36  Aligned_cols=56  Identities=14%  Similarity=0.142  Sum_probs=44.2

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      +-|...|.+|=..|.+.++.++|+..|.+-...| .-+...+..+-+.+=+.++..+
T Consensus       429 PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~LakLye~l~d~~e  484 (559)
T KOG1155|consen  429 PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAKLYEELKDLNE  484 (559)
T ss_pred             CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHhHHH
Confidence            4578889999999999999999999998887666 2255777778888777777766

>PRK14574 hmsH outer membrane protein; Provisional

Probab=82.83  E-value=10  Score=27.97  Aligned_cols=54  Identities=15%  Similarity=0.131  Sum_probs=34.7

Q ss_pred             HHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           14 MLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        14 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ...|...|++++|+++|+++.+..-. |...+..+...+...++.++  ..++....
T Consensus       109 A~ly~~~gdyd~Aiely~kaL~~dP~-n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~  164 (822)
T PRK14574        109 ARAYRNEKRWDQALALWQSSLKKDPT-NPDLISGMIMTQADAGRGGVVLKQATELAE  164 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHhhcCCHHHHHHHHHHhcc
Confidence            34566678888888888888765321 34455566677777777766  55555543

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=82.72  E-value=5.1  Score=22.94  Aligned_cols=51  Identities=10%  Similarity=0.130  Sum_probs=38.9

Q ss_pred             HHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhhcc
Q 042815           30 FMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQAA   84 (87)
Q Consensus        30 ~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~~~   84 (87)
                      ++.+....+.|+......-|++|-+..++..  ++|+.++.+    ..+...+|-.+
T Consensus        72 lN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K----~g~~k~~Y~y~  124 (149)
T KOG4077|consen   72 LNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDK----CGAQKQVYPYY  124 (149)
T ss_pred             HHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHh----cccHHHHHHHH
Confidence            3444556789999999999999999999988  999988876    44444455444

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

Probab=80.95  E-value=3.4  Score=28.82  Aligned_cols=44  Identities=9%  Similarity=0.178  Sum_probs=35.5

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCCC-HhhHHHHHHHHcccchhHH
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRPN-AVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~~~~~~~~~~~   60 (87)
                      .-|.++|++++|+..|.+-...  .|| .+-|...-.+|...|++++
T Consensus       123 N~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAcY~~lgd~~~  167 (606)
T KOG0547|consen  123 NKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAACYESLGDWEK  167 (606)
T ss_pred             hhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHHHHHHhhHHH
Confidence            4578899999999999997755  788 6677777777788888875

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=80.86  E-value=4.5  Score=22.04  Aligned_cols=49  Identities=18%  Similarity=0.255  Sum_probs=37.8

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815           12 AMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus        12 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .++....+++..-.|.++++.|.+.+...+..|.=--|+.+.+.|-+..
T Consensus        12 ~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~   60 (120)
T PF01475_consen   12 AILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK   60 (120)
T ss_dssp             HHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence            5677777777789999999999999888888877777777777776654

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

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

Probab=80.38  E-value=10  Score=26.67  Aligned_cols=63  Identities=5%  Similarity=-0.039  Sum_probs=47.7

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +||.-.|++.|..=.+-..++.|..+|.+..-.  .|++.+|--..+-=-+.|.+..  .+|+....
T Consensus       171 ~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~VyerAie  235 (677)
T KOG1915|consen  171 EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVYERAIE  235 (677)
T ss_pred             CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            588899999999999999999999999998754  5888888766655555666655  55555443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=80.23  E-value=9.9  Score=28.07  Aligned_cols=60  Identities=2%  Similarity=-0.092  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcC-----CCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRG-----PRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g-----~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +=-++-++|...+.+++|+.+|++.....     ..++......|+-++...+++++  .+.+.+..
T Consensus       329 ~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~  395 (822)
T PRK14574        329 ARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSE  395 (822)
T ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHh
Confidence            34467788888888999999998886432     12233345678888888888888  77777765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	87
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.87
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.86
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.83
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.8
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	98.61
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	98.36
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.27
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	97.19
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	97.1
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	97.06
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.05
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	97.02
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	96.91
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	96.84
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	96.78
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	96.62
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.58
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	96.5
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.47
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	96.39
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	96.36
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	96.29
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	96.29
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	96.29
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	96.28
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.26
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	96.25
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.22
2gw1_A	514	Mitochondrial precursor proteins import receptor;	96.15
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	96.15
2gw1_A	514	Mitochondrial precursor proteins import receptor;	96.13
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	96.13
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.12
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	96.06
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	96.01
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	95.99
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	95.97
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	95.97
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	95.96
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	95.93
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	95.9
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	95.86
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	95.85
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	95.83
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	95.82
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	95.82
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	95.77
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	95.77
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	95.76
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	95.73
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	95.71
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	95.71
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	95.7
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	95.69
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	95.67
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	95.65
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	95.62
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	95.59
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	95.58
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	95.5
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	95.47
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	95.43
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	95.42
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	95.42
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	95.42
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	95.38
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	95.37
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	95.36
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	95.32
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	95.28
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	95.24
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	95.22
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	95.07
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	95.05
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	94.99
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	94.95
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	94.95
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	94.86
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	94.78
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	94.69
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	94.56
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	94.55
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	94.51
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	94.48
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	94.27
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	94.23
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	94.22
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	94.2
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	94.12
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	94.05
3u4t_A	272	TPR repeat-containing protein; structural genomics	93.89
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	93.82
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	93.82
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	93.78
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	93.7
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	93.69
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	93.68
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	93.45
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	93.45
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	93.29
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	93.24
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	93.22
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.18
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	93.13
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	93.12
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	93.03
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	92.79
3u4t_A	272	TPR repeat-containing protein; structural genomics	92.77
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	92.7
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	92.7
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	92.41
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	92.36
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	92.32
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	92.2
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	92.12
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	92.01
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	91.99
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	91.97
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	91.89
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	91.85
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	91.81
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	91.77
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	91.46
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	91.15
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	91.13
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	90.87
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	90.63
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	90.58
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	90.53
2l6j_A	111	TPR repeat-containing protein associated with HSP;	90.52
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	90.38
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	90.34
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	90.01
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	89.99
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	89.71
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	89.52
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	89.43
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	88.94
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	88.81
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	88.75
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	88.68
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	88.33
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	88.29
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	87.69
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	87.56
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	87.51
4g1t_A	472	Interferon-induced protein with tetratricopeptide	87.44
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	87.24
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	86.97
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	86.89
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	86.88
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	86.83
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	86.71
3k9i_A	117	BH0479 protein; putative protein binding protein,	86.67
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	86.54
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	86.33
2b7e_A	59	PRE-mRNA processing protein PRP40; structural prot	86.25
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	86.2
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	86.15
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	86.13
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	85.49
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	85.07
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	84.95
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	84.7
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	84.67
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	83.79
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	83.75
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	83.65
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	83.27
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	82.59
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	81.65
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	81.08
2kat_A	115	Uncharacterized protein; NESG, structure, structur	80.61
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	80.31
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	80.23

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.87  E-value=2.6e-22  Score=139.14  Aligned_cols=80  Identities=18%  Similarity=0.174  Sum_probs=75.4

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchh-HH--HHHHhchhcccccccchhhh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIF-GV--TLMGIQPQNLWYYIDGQIDA   80 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~-~~--~~~~~m~~~~~~g~~~~~~~   80 (87)
                      .||++|||+||.|||+.|++++|.++|++|.+.|+.||.+||+++|.++|+.|.. +.  ++|+.|..+   |+.||..+
T Consensus       162 ~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~k---G~~PD~vt  238 (1134)
T 3spa_A          162 LLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQE---GLKLQALF  238 (1134)
T ss_dssp             TCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH---TCCSHHHH
T ss_pred             CCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHc---CCCCChhh
Confidence            5899999999999999999999999999999999999999999999999999985 44  899999998   99999999


Q ss_pred             hhcccc
Q 042815           81 WQAACQ   86 (87)
Q Consensus        81 ~~~~~~   86 (87)
                      |++++.
T Consensus       239 Y~~ll~  244 (1134)
T 3spa_A          239 TAVLLS  244 (1134)
T ss_dssp             HHSCCC
T ss_pred             cccccC
Confidence            998763

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.86  E-value=4.8e-22  Score=130.39  Aligned_cols=80  Identities=8%  Similarity=-0.005  Sum_probs=70.5

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAW   81 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~   81 (87)
                      .||.+|||+||.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++  ++|+.|...   |+.||..+|
T Consensus       102 ~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~---G~~Pd~~ty  178 (501)
T 4g26_A          102 VPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVES---EVVPEEPEL  178 (501)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCCCCHHHH
T ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhc---CCCCCHHHH
Confidence            478889999999999999999999999999888999999999999999999998888  888888887   889999999


Q ss_pred             hcccc
Q 042815           82 QAACQ   86 (87)
Q Consensus        82 ~~~~~   86 (87)
                      +++|+
T Consensus       179 ~~Li~  183 (501)
T 4g26_A          179 AALLK  183 (501)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88874

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.83  E-value=1.2e-20  Score=123.78  Aligned_cols=80  Identities=8%  Similarity=0.048  Sum_probs=76.9

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAW   81 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~   81 (87)
                      .||.++||+||.+|++.|++++|.++|++|.+.|+.||..||++||++|++.|++++  +++++|...   |..|+..||
T Consensus       137 ~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~---g~~ps~~T~  213 (501)
T 4g26_A          137 QPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDL---VRQVSKSTF  213 (501)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---TSSBCHHHH
T ss_pred             CCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHh---CCCcCHHHH
Confidence            589999999999999999999999999999999999999999999999999999999  999999988   999999999


Q ss_pred             hcccc
Q 042815           82 QAACQ   86 (87)
Q Consensus        82 ~~~~~   86 (87)
                      +.+++
T Consensus       214 ~~l~~  218 (501)
T 4g26_A          214 DMIEE  218 (501)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98753

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.80  E-value=3.4e-20  Score=128.74  Aligned_cols=76  Identities=9%  Similarity=0.059  Sum_probs=72.1

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHH---HcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIE---KRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQ   82 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~---~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~   82 (87)
                      +|||+||.|||+.|++++|.++|.+|.   ..|+.||.+|||+||+++|+.|++++  ++|+.|...   |+.||.+|||
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~---G~~PDvvTYn  204 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDA---GLTPDLLSYA  204 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT---TCCCCHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHc---CCCCcHHHHH
Confidence            689999999999999999999998876   46899999999999999999999999  999999998   9999999999


Q ss_pred             cccc
Q 042815           83 AACQ   86 (87)
Q Consensus        83 ~~~~   86 (87)
                      ++|+
T Consensus       205 tLI~  208 (1134)
T 3spa_A          205 AALQ  208 (1134)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9985

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=98.61  E-value=5.2e-08  Score=63.59  Aligned_cols=77  Identities=5%  Similarity=-0.153  Sum_probs=63.7

Q ss_pred             CCCCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhh
Q 042815            2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQID   79 (87)
Q Consensus         2 m~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~   79 (87)
                      +|.+++..|+.++.+|.+.|++++|..+|++|..  ..||..++..+..+|.+.|++++  .+|+.+..     ..++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~  151 (597)
T 2xpi_A           79 DSLSREDYLRLWRHDALMQQQYKCAAFVGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDL-----YNRSSA  151 (597)
T ss_dssp             ---CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCG-----GGTCHH
T ss_pred             chHHHHHHHHHHHHHHHHccCchHHHHHHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhc-----cccchh
Confidence            4567899999999999999999999999999984  46888999999999999999998  78887753     356677


Q ss_pred             hhhccc
Q 042815           80 AWQAAC   85 (87)
Q Consensus        80 ~~~~~~   85 (87)
                      +++.++
T Consensus       152 ~~~~l~  157 (597)
T 2xpi_A          152 CRYLAA  157 (597)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=98.36  E-value=1.3e-06  Score=57.04  Aligned_cols=63  Identities=13%  Similarity=0.126  Sum_probs=38.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCCC--HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRPN--AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~pd--~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      |..+|+.+...|.+.|++++|.++|+++.+.    +..|+  ..+|..+..+|.+.|++++  ..++.+..
T Consensus       474 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  544 (597)
T 2xpi_A          474 DPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLL  544 (597)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            4556666666666666666666666666544    55565  4566666666666666666  55555554

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.27  E-value=0.0014  Score=33.59  Aligned_cols=60  Identities=15%  Similarity=0.061  Sum_probs=31.3

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...|..+...|.+.|++++|.++|.++.... ..+..++..+...+...|+.++  ..++...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~   70 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKAL   70 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4455555555666666666666666555432 1234445555555555555555  4444443

>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=97.19  E-value=0.0026  Score=32.84  Aligned_cols=62  Identities=13%  Similarity=0.055  Sum_probs=39.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+...|.+.|++++|..+|+++...+ ..+...+..+...+...|+.++  ..++.+..
T Consensus        34 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~   97 (136)
T 2fo7_A           34 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE   97 (136)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            45566666677777777777777777766543 2244566666666777777666  55555543

>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=97.10  E-value=0.0027  Score=39.39  Aligned_cols=26  Identities=8%  Similarity=0.096  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIE   34 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~   34 (87)
                      +|+.+...|.+.|++++|.+.|+++.
T Consensus       273 ~~~~l~~~~~~~g~~~~A~~~~~~al  298 (388)
T 1w3b_A          273 AYCNLANALKEKGSVAEAEDCYNTAL  298 (388)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33334444444444444444444433

>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=97.06  E-value=0.0024  Score=39.59  Aligned_cols=62  Identities=6%  Similarity=0.037  Sum_probs=50.5

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +..+|+.+...|.+.|++++|.+.|+++....  | +..+|..+...+.+.|+.++  ..++.+...
T Consensus       236 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  300 (388)
T 1w3b_A          236 HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANALKEKGSVAEAEDCYNTALRL  300 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            56788999999999999999999999988653  4 45678888888888888888  777776653

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.05  E-value=0.0057  Score=31.23  Aligned_cols=64  Identities=14%  Similarity=0.063  Sum_probs=52.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+...|.+.|++++|..+|+++.... ..+..++..+-..+...|+.++  ..++.....
T Consensus        41 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           41 NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            356788999999999999999999999998764 3366788888899999999988  777776643

>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=97.02  E-value=0.0072  Score=31.09  Aligned_cols=63  Identities=14%  Similarity=0.079  Sum_probs=51.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+...|.+.|++++|..+|+++.... ..+...+..+...+...|+.++  ..+..+..
T Consensus        67 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           67 RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            356788899999999999999999999998764 2356788888899999999988  67766654

>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=96.91  E-value=0.00014  Score=47.63  Aligned_cols=56  Identities=7%  Similarity=0.078  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH-HHHHhchhc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV-TLMGIQPQN   69 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~-~~~~~m~~~   69 (87)
                      .+|+.|..++.+.|++++|++.|.+      .+|..+|..++.++...|++++ ..+..|..+
T Consensus        33 ~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark   89 (449)
T 1b89_A           33 AVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQMARK   89 (449)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4899999999999999999999976      3578889999999999998888 335555544

>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=96.84  E-value=0.0032  Score=39.55  Aligned_cols=62  Identities=11%  Similarity=0.025  Sum_probs=34.7

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+...|.+.|++++|+.+|+++.... ..+..++..+..++...|+.++  ..|+.+..
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   88 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQ   88 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            44556666666666666666666666655432 2245555555566666666555  55554443

>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=96.78  E-value=0.007  Score=38.02  Aligned_cols=64  Identities=5%  Similarity=-0.176  Sum_probs=55.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+..+|..+...|.+.|++++|...|+++.+.+ ..+...+..+..++.+.|++++  ..|+.+...
T Consensus        58 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  123 (450)
T 2y4t_A           58 DNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS  123 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             ccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            467899999999999999999999999998775 2357789999999999999988  888887654

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=96.62  E-value=0.021  Score=31.61  Aligned_cols=72  Identities=8%  Similarity=0.004  Sum_probs=56.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQ   82 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~   82 (87)
                      .+...|..+-..|.+.|++++|++.|++..+.. .-+...|..+-.++.+.|+.++  ..|++...     +.|+...|+
T Consensus       105 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-----~~p~~a~~~  178 (184)
T 3vtx_A          105 VYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKKALE-----KEEKKAKYE  178 (184)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-----TTHHHHHHC
T ss_pred             cchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHHHHh-----CCccCHHHH
Confidence            456788888899999999999999999988664 2256688888899999999988  77777654     356655554

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.58  E-value=0.012  Score=30.59  Aligned_cols=63  Identities=10%  Similarity=-0.083  Sum_probs=50.6

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...|..+-..|.+.|++++|+..|++..+..-. +...+..+-.++...|+.++  ..+......
T Consensus        26 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~   90 (117)
T 3k9i_A           26 LAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQGVELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4567888999999999999999999998876422 46677888888899999988  666666543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=96.50  E-value=0.011  Score=33.38  Aligned_cols=60  Identities=7%  Similarity=-0.296  Sum_probs=28.0

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHccc-chhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKI-KIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~-~~~~~--~~~~~m~   67 (87)
                      ...|..+...|.+.|++++|.+.|++..... ..+..++..+...+... |+.++  ..++...
T Consensus        42 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~  104 (225)
T 2vq2_A           42 ELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKAL  104 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            3444445555555555555555555544332 11333444444555555 55544  4444433

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.47  E-value=0.024  Score=28.77  Aligned_cols=62  Identities=15%  Similarity=0.126  Sum_probs=49.9

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .|...|..+-..|.+.|++++|+..|++..+..-. +...|..+-.++...|+.++  ..+++..
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVETDPD-YVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            36678899999999999999999999998876422 45578888888999999888  6666544

>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=96.39  E-value=0.012  Score=34.10  Aligned_cols=20  Identities=5%  Similarity=0.066  Sum_probs=7.4

Q ss_pred             HHHHHHhcCCchhHHHHHHH
Q 042815           13 MMLGLAKNGKNGMGVELFMS   32 (87)
Q Consensus        13 li~~~~~~g~~~~a~~l~~~   32 (87)
                      +...|.+.|++++|.+.|++
T Consensus        77 la~~~~~~~~~~~A~~~~~~   96 (252)
T 2ho1_A           77 LAVVFQTEMEPKLADEEYRK   96 (252)
T ss_dssp             HHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHH
Confidence            33333333333333333333

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=96.36  E-value=0.035  Score=28.61  Aligned_cols=62  Identities=13%  Similarity=0.022  Sum_probs=36.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+...|..+-..|.+.|++++|...|++..... ..+...+..+-..+...|+.++  ..++...
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~   77 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECI   77 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            345566666666666777777777766655432 1144555566666666666665  4554444

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=96.29  E-value=0.014  Score=35.74  Aligned_cols=62  Identities=5%  Similarity=-0.054  Sum_probs=45.1

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +..+|..+...|.+.|++++|...|++..+.. ..+..+|..+-.++...|+.++  ..|+....
T Consensus       212 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  275 (365)
T 4eqf_A          212 DPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALE  275 (365)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            56677788888888888888888888877553 2256677777788888888777  66666554

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=96.29  E-value=0.015  Score=29.05  Aligned_cols=52  Identities=10%  Similarity=-0.150  Sum_probs=22.7

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC--CHhhHHHHHHHHccc-chhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP--NAVTFVGVLTAYGKI-KIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p--d~~t~~~ll~~~~~~-~~~~~   60 (87)
                      ..|..+-..|.+.|++++|...|++..+.. ..  +...+..+-.++... |+.++
T Consensus        41 ~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~   95 (112)
T 2kck_A           41 KYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADALRYIEGKEVE   95 (112)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHHTTCSSCSHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHHHHHhCCHHH
Confidence            344444444444555555555554444321 11  233444444444444 44444

>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=96.29  E-value=0.029  Score=30.49  Aligned_cols=59  Identities=14%  Similarity=0.134  Sum_probs=28.4

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      ...|..+...|.+.|++++|.+.|++..... ..+...+..+...+...|+.++  ..++..
T Consensus        76 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~  136 (186)
T 3as5_A           76 VKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIA  136 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHH
Confidence            3445555555555555555555555554332 1233444444455555555544  444443

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=96.28  E-value=0.024  Score=31.94  Aligned_cols=62  Identities=11%  Similarity=0.054  Sum_probs=33.1

Q ss_pred             cHhHHHHHHHHHHhc-CCchhHHHHHHHHHHcCCCCC-HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKN-GKNGMGVELFMSIEKRGPRPN-AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~-g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+...|.+. |++++|...|++....+..|+ ...+..+-..+...|+.++  ..++...
T Consensus        75 ~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  140 (225)
T 2vq2_A           75 SAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSL  140 (225)
T ss_dssp             CHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            344555566666666 666666666666555222232 3355555555555565555  4444443

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.26  E-value=0.031  Score=27.05  Aligned_cols=63  Identities=14%  Similarity=0.054  Sum_probs=49.8

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...|..+-..|.+.|++++|...|++..... ..+...+..+-..+...|+.++  ..++.....
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            45678888889999999999999999987654 2256677788888888999888  667666543

>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=96.25  E-value=0.029  Score=30.46  Aligned_cols=64  Identities=14%  Similarity=0.135  Sum_probs=47.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+...|.+.|++++|...|++..... ..+...+..+...+...|+.++  ..++.....
T Consensus        40 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  105 (186)
T 3as5_A           40 FDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEA  105 (186)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            356778888888888899999999888887653 2356677777777888888877  666665543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.22  E-value=0.043  Score=28.16  Aligned_cols=63  Identities=3%  Similarity=-0.183  Sum_probs=50.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+-..|.+.|++++|+..|++..... ..+...|..+-.++...|+.++  ..|+....
T Consensus        17 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           17 DNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            467789999999999999999999999988664 2245678888888888898888  66665543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=96.15  E-value=0.014  Score=37.04  Aligned_cols=64  Identities=13%  Similarity=0.005  Sum_probs=41.2

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ||...|..+...|.+.|++++|...|+++.... ..+...+..+..++...|+.++  ..|+.+...
T Consensus        37 p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  102 (514)
T 2gw1_A           37 EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFDLSVLSLN  102 (514)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            466667777777777777777777777766543 1244566666677777777766  666655543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=96.15  E-value=0.017  Score=35.09  Aligned_cols=35  Identities=11%  Similarity=-0.033  Sum_probs=16.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP   40 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p   40 (87)
                      +..++..+...|.+.|+.++|++.|+++...+..|
T Consensus        64 ~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P   98 (291)
T 3mkr_A           64 ELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDV   98 (291)
T ss_dssp             HHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCC
T ss_pred             hHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCC
Confidence            34444444445555555555555555544444334

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=96.13  E-value=0.024  Score=36.02  Aligned_cols=62  Identities=8%  Similarity=-0.023  Sum_probs=52.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...|-..-..|.+.|++++|+..|.++....  ||...+..+..++.+.|+++.  ..++.....
T Consensus         5 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   68 (514)
T 2gw1_A            5 YALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALEL   68 (514)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhcc
Confidence            34566777788999999999999999998775  899999999999999999988  777777654

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=96.13  E-value=0.033  Score=34.08  Aligned_cols=61  Identities=10%  Similarity=0.001  Sum_probs=37.1

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +..+|..+...|.+.|++++|+..|++..... ..+..++..+-..+...|+.++  ..++...
T Consensus        98 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  160 (365)
T 4eqf_A           98 DAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYTNTSHQQDACEALKNWI  160 (365)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHccccHHHHHHHHHHHH
Confidence            45566666666666666666666666665543 1235566666666666666666  5555544

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.12  E-value=0.045  Score=27.46  Aligned_cols=63  Identities=13%  Similarity=0.040  Sum_probs=49.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ++...|..+-..+.+.|++++|.+.|++..... ..+...+..+-.++...|+.++  ..++....
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            356678888888999999999999999987653 2256677788888888999888  66776654

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=96.06  E-value=0.053  Score=27.88  Aligned_cols=64  Identities=9%  Similarity=-0.078  Sum_probs=51.7

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|...|++..... ..+...+..+-.++...|+.++  ..++.....
T Consensus        48 ~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           48 KDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDL  113 (133)
T ss_dssp             TCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            467788999999999999999999999988764 2256688888888899999988  777766543

>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=96.01  E-value=0.041  Score=31.79  Aligned_cols=52  Identities=12%  Similarity=-0.026  Sum_probs=21.2

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ..|..+...|.+.|++++|...|++..... ..+...+..+...+...|+.++
T Consensus       142 ~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          142 RVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHH
Confidence            334444444444444444444444443322 1123334444444444444443

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=95.99  E-value=0.047  Score=31.19  Aligned_cols=52  Identities=13%  Similarity=0.111  Sum_probs=23.5

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ..|..+...|.+.|++++|...|++..... ..+..++..+-..+...|+.++
T Consensus       160 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  211 (243)
T 2q7f_A          160 EARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREK  211 (243)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHH
Confidence            344444444455555555555555444332 1123344444444444444444

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=95.97  E-value=0.049  Score=31.10  Aligned_cols=61  Identities=10%  Similarity=0.071  Sum_probs=30.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+...|.+.|++++|...|++..... ..+...+..+...+...|+.+.  ..++...
T Consensus        56 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  118 (243)
T 2q7f_A           56 DAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVVKEMYKEAKDMFEKAL  118 (243)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            34455555555555555555555555554432 1234444555555555555554  4444433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=95.97  E-value=0.028  Score=32.76  Aligned_cols=60  Identities=8%  Similarity=-0.132  Sum_probs=32.0

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...|..+-..|.+.|++++|...|++..... ..+...+..+-..+...|++++  ..++...
T Consensus        43 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al  104 (275)
T 1xnf_A           43 AQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVL  104 (275)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            4455555555666666666666666655442 1134455555555555555555  4444443

>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=95.96  E-value=0.032  Score=33.98  Aligned_cols=62  Identities=6%  Similarity=-0.014  Sum_probs=47.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +..+|..+...|.+.|++++|...|++..... ..+..++..+-..+...|+.++  ..++....
T Consensus       216 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  279 (368)
T 1fch_A          216 DPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALE  279 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            46778888888888888888888888877653 2246678888888888888877  66766654

>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=95.93  E-value=0.067  Score=27.92  Aligned_cols=55  Identities=15%  Similarity=-0.035  Sum_probs=28.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .+...|..+-..|.+.|++++|...|.+..... ..+...+..+-.++...|+.+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~   61 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQ   61 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHH
Confidence            344555555555555566666666555554432 1133444455555555555554

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=95.90  E-value=0.05  Score=31.65  Aligned_cols=63  Identities=11%  Similarity=-0.129  Sum_probs=47.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+-..|.+.|++++|...|++..... ..+...+..+-..+...|+.++  ..++....
T Consensus        75 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  139 (275)
T 1xnf_A           75 DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  139 (275)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            356778888888888888888888888887653 2256677778888888888877  66666654

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=95.86  E-value=0.059  Score=26.75  Aligned_cols=64  Identities=6%  Similarity=-0.051  Sum_probs=51.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|...|++..... ..+...+..+-..+...|+.++  ..++.....
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~   69 (112)
T 2kck_A            4 QNPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINV   69 (112)
T ss_dssp             SSTTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            456678888888999999999999999988664 2356678888888889999988  777776654

>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=95.85  E-value=0.043  Score=32.68  Aligned_cols=62  Identities=5%  Similarity=-0.120  Sum_probs=43.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+...|.+.|++++|...|++..... ..+..++..+-..+...|+.++  ..++....
T Consensus       171 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  234 (327)
T 3cv0_A          171 DAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALD  234 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            55677777778888888888888888876553 2245677777777777777777  66666554

>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=95.83  E-value=0.061  Score=26.90  Aligned_cols=61  Identities=11%  Similarity=-0.094  Sum_probs=37.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|.+.|++++|...|++..... ..+...+..+-.++...|+.++  ..++...
T Consensus        37 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~   99 (118)
T 1elw_A           37 NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGL   99 (118)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            45566666666777777777777777766543 1244556666666666776666  5555544

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=95.82  E-value=0.04  Score=31.81  Aligned_cols=62  Identities=8%  Similarity=-0.111  Sum_probs=52.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...|..+=..|.+.|++++|+..|++..+..  .+...+..+-.++...|+.++  ..|+.....
T Consensus       117 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  180 (217)
T 2pl2_A          117 YAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQ  180 (217)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            56778888888999999999999999998777  688888888889999999988  777776643

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=95.82  E-value=0.082  Score=28.00  Aligned_cols=61  Identities=7%  Similarity=-0.109  Sum_probs=37.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|.+.|++++|+..|++..+.. ..+...|..+-.++...|++++  ..|+...
T Consensus        46 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al  108 (126)
T 4gco_A           46 NAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVAMREWSKAQRAYEDAL  108 (126)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45566666666777777777777777665543 1234456666666666666666  5555544

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.77  E-value=0.083  Score=27.73  Aligned_cols=61  Identities=13%  Similarity=-0.024  Sum_probs=37.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC----HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN----AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+...|..+-..+.+.|++++|...|++....  .|+    ...+..+-.++...|++++  ..++...
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~   92 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAI   92 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            35566666667777777777777777776543  344    4555556666666666666  4555444

>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=95.77  E-value=0.07  Score=32.45  Aligned_cols=61  Identities=5%  Similarity=-0.007  Sum_probs=35.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +..+|..+...|.+.|++++|...|++..... ..+..++..+...+...|+.++  ..++...
T Consensus        97 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  159 (368)
T 1fch_A           97 HMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWL  159 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44556666666666666666666666665443 2245556666666666666655  5555444

>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=95.76  E-value=0.048  Score=32.45  Aligned_cols=64  Identities=8%  Similarity=0.055  Sum_probs=52.7

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+...|.+.|++++|...|++..... ..+..++..+-..+...|+.++  ..++.....
T Consensus       204 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  269 (327)
T 3cv0_A          204 DDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYM  269 (327)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            456789999999999999999999999988664 2356788889999999999988  777766543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=95.73  E-value=0.057  Score=32.78  Aligned_cols=52  Identities=4%  Similarity=-0.031  Sum_probs=25.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIF   58 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~   58 (87)
                      +...|+.+-..|.+.|++++|.+.|++..... .-|..++..+...+...|+.
T Consensus       199 ~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~~~l~~l~~~~~~~g~~  250 (291)
T 3mkr_A          199 TLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHPETLINLVVLSQHLGKP  250 (291)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCC
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCC
Confidence            34445555555555555555555555544332 11333444444444445544

>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=95.71  E-value=0.023  Score=37.33  Aligned_cols=46  Identities=17%  Similarity=0.039  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .|..+..++.+.|++++|.+.|+++      .+..+|..++.+|...|+++.
T Consensus       150 n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~l  195 (449)
T 1b89_A          150 NFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRL  195 (449)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHH
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHH
Confidence            3445555555555555555555544      155566666666666654443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=95.71  E-value=0.056  Score=29.91  Aligned_cols=51  Identities=12%  Similarity=0.053  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .|..+=..|.+.|++++|+..|++..... .-+...|..+=.++...|+.++
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~   88 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQ   88 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHH
Confidence            34444444444555555555555544332 1133344444444444444444

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=95.70  E-value=0.051  Score=31.21  Aligned_cols=61  Identities=8%  Similarity=-0.092  Sum_probs=52.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ....|..+-..|.+.|++++|..+|++..+..  .+...+..+-.++...|+.++  ..++....
T Consensus         4 ~a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~   66 (258)
T 3uq3_A            4 MADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVE   66 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            34578888899999999999999999999877  788899999999999999988  66666654

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=95.69  E-value=0.096  Score=27.98  Aligned_cols=61  Identities=5%  Similarity=-0.218  Sum_probs=34.7

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|.+.|++++|+..|++..... .-+...+..+-.++...|+.++  ..|+...
T Consensus        51 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  113 (142)
T 2xcb_A           51 DARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGDLDGAESGFYSAR  113 (142)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44556666666666666666666666665443 1133445555556666666665  4555443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=95.67  E-value=0.076  Score=29.37  Aligned_cols=63  Identities=6%  Similarity=-0.079  Sum_probs=52.9

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .|...|..+=..|.+.|++++|+..|++.....  | +...|..+=.++...|+.++  ..|+.....
T Consensus        68 ~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~--P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A           68 YNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG--KNDYTPVFHTGQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--SSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            467889999999999999999999999988664  4 45678888889999999998  777776654

>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=95.65  E-value=0.064  Score=29.22  Aligned_cols=61  Identities=3%  Similarity=-0.132  Sum_probs=32.5

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|.+.|++++|+..|++..... .-+...+..+-.++...|+.++  ..|+...
T Consensus        54 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  116 (148)
T 2vgx_A           54 DSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQXGELAEAESGLFLAQ  116 (148)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44555555555666666666666666655432 1133445555555556666655  4444443

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=95.62  E-value=0.055  Score=32.79  Aligned_cols=63  Identities=3%  Similarity=-0.114  Sum_probs=49.0

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh--hHHHHHHHHcccchhHH--HHHHhchh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV--TFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~--t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +.+...|..+...+.+.|++++|.++|++..+  +.|+..  .|..+...+.+.|+++.  .+|++...
T Consensus        96 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~  162 (308)
T 2ond_A           96 KKNMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE  162 (308)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            34566899999999999999999999999876  456533  68888888888888877  77776654

>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=95.59  E-value=0.1  Score=28.36  Aligned_cols=64  Identities=6%  Similarity=0.053  Sum_probs=51.0

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..+.+.|++++|...|++..... ..+...|..+-.++...|+.++  ..|+.....
T Consensus        19 ~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l   84 (148)
T 2vgx_A           19 DTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM   84 (148)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            356678888889999999999999999987664 2266678788888889999988  777776643

>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=95.58  E-value=0.025  Score=28.96  Aligned_cols=63  Identities=14%  Similarity=0.082  Sum_probs=34.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCC--CCC----HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGP--RPN----AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~--~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|...|.+.....-  .++    ..++..+-..+...|+.+.  ..|+....
T Consensus        37 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           37 NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            445566666666666666666666666554321  111    4455555556666666655  55554443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=95.50  E-value=0.096  Score=26.60  Aligned_cols=61  Identities=8%  Similarity=-0.110  Sum_probs=32.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|.+.|++++|...|.+..... ..+...+..+-..+...|+.+.  ..++...
T Consensus        45 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  107 (131)
T 2vyi_A           45 NAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSSLNKHVEAVAYYKKAL  107 (131)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            34455555556666666666666666655432 1134455555555555565555  4444443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=95.47  E-value=0.12  Score=28.09  Aligned_cols=53  Identities=8%  Similarity=-0.109  Sum_probs=24.7

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ...|..+-..|.+.|++++|+..|++..... .-+...|..+-.++...|+.++
T Consensus        45 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~   97 (164)
T 3sz7_A           45 PIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLARFDMADYKG   97 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccCHHH
Confidence            3444445555555555555555555544332 1123344444444444555444

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=95.43  E-value=0.079  Score=34.50  Aligned_cols=71  Identities=17%  Similarity=0.111  Sum_probs=56.0

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAW   81 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~   81 (87)
                      .|...|..++. +.+.|++++|..+|+++.+.  .| +...|...+..+.+.|+.+.  .+|++....     .|+...|
T Consensus        11 ~~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~--~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~-----~p~~~lw   82 (530)
T 2ooe_A           11 YDLDAWSILIR-EAQNQPIDKARKTYERLVAQ--FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK-----VLHIDLW   82 (530)
T ss_dssp             TCHHHHHHHHH-HHHSSCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT-----CCCHHHH
T ss_pred             CCHHHHHHHHH-HHHhCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-----CCChHHH
Confidence            36789999998 58899999999999998754  45 45578889999988998888  888888765     3565555


Q ss_pred             hc
Q 042815           82 QA   83 (87)
Q Consensus        82 ~~   83 (87)
                      ..
T Consensus        83 ~~   84 (530)
T 2ooe_A           83 KC   84 (530)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=95.42  E-value=0.11  Score=29.69  Aligned_cols=54  Identities=17%  Similarity=0.009  Sum_probs=27.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      +...|..+-..|.+.|++++|...|++..... ..+...+..+-..+...|+.++
T Consensus       172 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~  225 (258)
T 3uq3_A          172 DARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYAS  225 (258)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHH
Confidence            34455555555555555555555555554432 1134445555555555555554

>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=95.42  E-value=0.11  Score=26.86  Aligned_cols=61  Identities=15%  Similarity=0.006  Sum_probs=39.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...|..+-..|.+.|++++|+..|++..... .-+...|..+-.++...|+.++  ..|+...
T Consensus        37 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al   99 (126)
T 3upv_A           37 DARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDAAR   99 (126)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhCHHHHHHHHHHHH
Confidence            45667777777777777777777777766543 1134566666666667777766  5555444

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=95.42  E-value=0.094  Score=28.91  Aligned_cols=61  Identities=13%  Similarity=0.056  Sum_probs=45.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+=..|.+.|++++|++.|++..+..  | +...+..+-.++.+.|+.++  ..+.....
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~   67 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD--PNNVETLLKLGKTYMDIGLPNDAIESLKKFVV   67 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            45678888888888899999999998877653  4 55677777788888888877  55554443

>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=95.38  E-value=0.11  Score=26.46  Aligned_cols=62  Identities=8%  Similarity=-0.025  Sum_probs=49.2

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ...|..+-..|.+.|++++|...|.+..... ..+...+..+-..+...|+.++  ..++.....
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~   67 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEV   67 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhh
Confidence            4578888889999999999999999988664 3356678888888888898888  666665543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=95.37  E-value=0.094  Score=28.02  Aligned_cols=63  Identities=11%  Similarity=0.084  Sum_probs=49.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...+..+-..+.+.|++++|...|++..... ..+...|..+-.++...|+.++  ..|+.....
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   81 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALM   81 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            45567777788999999999999999988664 2266677778888888999988  777766643

>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=95.36  E-value=0.067  Score=31.84  Aligned_cols=60  Identities=7%  Similarity=0.024  Sum_probs=28.6

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...|..+-..|.+.|++++|...|++.....- .+...+..+-..+...|+.++  ..+....
T Consensus       125 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al  186 (330)
T 3hym_B          125 GPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYGLTNNSKLAERFFSQAL  186 (330)
T ss_dssp             THHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            34455555555555555555555555544321 122334444445555555554  4444433

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=95.32  E-value=0.11  Score=28.33  Aligned_cols=64  Identities=6%  Similarity=-0.002  Sum_probs=52.0

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|+..|++..... .-+...|..+-.++...|++++  ..|+.....
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~   74 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVV   74 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            456788888899999999999999999988664 2266788888889999999988  777766543

>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=95.28  E-value=0.083  Score=31.44  Aligned_cols=64  Identities=9%  Similarity=-0.119  Sum_probs=52.7

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|...|++..+.. ..+...+..+-..+.+.|+.++  ..++.....
T Consensus       234 ~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  299 (330)
T 3hym_B          234 KWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALGL  299 (330)
T ss_dssp             TCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHcc
Confidence            345789999999999999999999999988764 2256688888899999999988  777776643

>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=95.24  E-value=0.15  Score=28.64  Aligned_cols=64  Identities=8%  Similarity=-0.058  Sum_probs=49.8

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .|+...|..+-..|.+.|++++|+..|++..... ..+...+..+-.++...|+.++  ..|+....
T Consensus        34 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   99 (213)
T 1hh8_A           34 DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALI   99 (213)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            3467788888899999999999999999987654 2356677788888888888888  66666554

>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=95.22  E-value=0.12  Score=25.82  Aligned_cols=63  Identities=11%  Similarity=-0.053  Sum_probs=49.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...|..+...+.+.|++++|...|++..... ..+...+..+-..+...|+.++  ..+......
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   67 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL   67 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            45678888899999999999999999987653 2256677777788888888887  666665543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=95.07  E-value=0.14  Score=25.96  Aligned_cols=64  Identities=16%  Similarity=0.015  Sum_probs=50.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..+...|++++|...|++..... ..+...+..+-..+...|+.++  ..++.....
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   75 (131)
T 2vyi_A           10 AEAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICI   75 (131)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhc
Confidence            356788888999999999999999999988653 2356778888888888998888  666666543

>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=95.05  E-value=0.097  Score=28.98  Aligned_cols=60  Identities=8%  Similarity=0.056  Sum_probs=40.8

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGI   65 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~   65 (87)
                      +...|..+-..|.+.|++++|...|++.....-.+ +...+..+...+...|+.++  ..|.+
T Consensus       107 ~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~  169 (176)
T 2r5s_A          107 NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRR  169 (176)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHH
Confidence            45677777778888888888888888876553322 24466677777777777765  44443

>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=94.99  E-value=0.17  Score=28.86  Aligned_cols=53  Identities=11%  Similarity=-0.009  Sum_probs=26.1

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ..|...=..|.+.|++++|+..|++.....-.+|...+..+-.++...|+.++
T Consensus         8 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~   60 (228)
T 4i17_A            8 NQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKE   60 (228)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHH
Confidence            44444444555555555555555555544322344444444444455555544

>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=94.95  E-value=0.17  Score=26.31  Aligned_cols=63  Identities=5%  Similarity=-0.163  Sum_probs=50.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+-..|.+.|++++|...|++..... .-+...+..+-.++...|+.+.  ..|.....
T Consensus        41 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           41 LVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            356788999999999999999999999988764 2256688888888889999988  66666553

>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=94.95  E-value=0.19  Score=26.83  Aligned_cols=62  Identities=6%  Similarity=-0.070  Sum_probs=36.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|...|.+..... ..+...+..+-.++...|+.++  ..++....
T Consensus        46 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~  109 (166)
T 1a17_A           46 NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVK  109 (166)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            45566666666677777777777777665442 1234455556666666666666  55555443

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=94.86  E-value=0.19  Score=26.33  Aligned_cols=53  Identities=11%  Similarity=0.111  Sum_probs=25.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~   60 (87)
                      +...|..+=..+.+.|++++|+..|++..+..  | +...+..+-.++...|+.++
T Consensus        50 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~la~~~~~~g~~~~  103 (121)
T 1hxi_A           50 REEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEHNANA  103 (121)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHH
Confidence            33444444445555555555555555544332  2 23344444444555555544

>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=94.78  E-value=0.13  Score=27.97  Aligned_cols=52  Identities=12%  Similarity=0.064  Sum_probs=24.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFG   59 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~   59 (87)
                      +..+|..+-..|.+.|++++|+..|++..+.  .| +...+..+-..+.+.|+.+
T Consensus        64 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~  116 (150)
T 4ga2_A           64 DPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCKNDVTD  116 (150)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChH
Confidence            3444555555555555555555555554433  22 2334444444444444443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.69  E-value=0.21  Score=26.10  Aligned_cols=62  Identities=6%  Similarity=-0.170  Sum_probs=49.4

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ...|..+-..|.+.|++++|+..|++..... ..+...+..+-.++...|+.++  ..|+.....
T Consensus        65 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           65 AVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            6788888999999999999999999987653 2256677778888888898888  777766543

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=94.56  E-value=0.21  Score=30.23  Aligned_cols=63  Identities=13%  Similarity=0.029  Sum_probs=41.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcC-CCCC--HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRG-PRPN--AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd--~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..++..+.+.|++++|..+|++..... +.|+  ...|..++....+.|+.+.  .++.+...
T Consensus       202 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~  269 (308)
T 2ond_A          202 IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45677777777777888888888888877653 4553  4466666666666677666  55555443

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=94.55  E-value=0.083  Score=31.16  Aligned_cols=63  Identities=13%  Similarity=0.093  Sum_probs=49.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc-------CCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR-------GPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-------g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +..+|..+-..|...|++++|..+|++....       .-......+..+-..+...|++++  ..++....
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   97 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALA   97 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4578999999999999999999999998763       222345577888888888999888  66655543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=94.51  E-value=0.2  Score=28.82  Aligned_cols=63  Identities=11%  Similarity=0.056  Sum_probs=50.1

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ++...|..+-..+.+.|++++|...|++..+.  .| +...+..+-..+...|+.++  ..+++....
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~   68 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKE--NPQDPEALYWLARTQLKLGLVNPALENGKTLVAR   68 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--SSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            36667888888999999999999999998755  44 56678888888889999988  777776643

>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=94.48  E-value=0.23  Score=25.64  Aligned_cols=62  Identities=13%  Similarity=0.040  Sum_probs=49.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+=..+.+.|++++|+..|.+..... ..+...|..+-.++.+.|++++  ..++....
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~   66 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIE   66 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            34567777788999999999999999987664 2366788888888999999988  66766654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=94.27  E-value=0.2  Score=32.47  Aligned_cols=61  Identities=10%  Similarity=-0.036  Sum_probs=44.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHccc---------chhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKI---------KIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~---------~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|.+.|++..+.  .|+...+..+-..+...         |++++  ..+++...
T Consensus       136 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~  207 (474)
T 4abn_A          136 LVEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQ  207 (474)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHH
Confidence            4567777888888888888888888886654  46667777777777777         77776  66665554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=94.23  E-value=0.22  Score=29.83  Aligned_cols=62  Identities=5%  Similarity=-0.195  Sum_probs=40.8

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|...|++..... .-+...+..+-..+...|+.++  ..++....
T Consensus        36 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~   99 (359)
T 3ieg_A           36 NYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLK   99 (359)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCChHHHHHHHHHHHh
Confidence            45567777777777777777777777766543 1144566667777777777766  66665554

>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=94.22  E-value=0.34  Score=27.60  Aligned_cols=62  Identities=16%  Similarity=0.086  Sum_probs=47.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +|...|..+-..|.+.|++++|+..|++....  .| +...+..+-..+...|+.++  ..++....
T Consensus        40 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  104 (228)
T 4i17_A           40 QDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKSAAYRDMKNNQEYIATLTEGIK  104 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            56667777888889999999999999997755  44 45577778888888888887  66666654

>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=94.20  E-value=0.17  Score=32.89  Aligned_cols=53  Identities=9%  Similarity=-0.158  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHH-----cC-CCCCHh-hHHHHHHHHcccchhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEK-----RG-PRPNAV-TFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~g-~~pd~~-t~~~ll~~~~~~~~~~~   60 (87)
                      .++|.|-..|...|++++|+.++++..+     .| -.|++. +++.+-..|...|+.++
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~e  400 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAA  400 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHH
Confidence            6899999999999999999999999763     23 345555 78899999999999988

>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=94.12  E-value=0.1  Score=29.37  Aligned_cols=61  Identities=10%  Similarity=0.022  Sum_probs=49.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...+..+-..+.+.|++++|...|.+.    +.|+...+..+-..+...|+.++  ..++.....
T Consensus         4 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   66 (213)
T 1hh8_A            4 VEAISLWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINR   66 (213)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            34556677777889999999999999886    36788899999999999999988  677666543

>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=94.05  E-value=0.17  Score=29.22  Aligned_cols=62  Identities=19%  Similarity=0.114  Sum_probs=49.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc------CCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR------GPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~------g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...+|..+-..|...|++++|...|++....      +-.| ...++..+-..+...|++++  ..+....
T Consensus        42 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  112 (283)
T 3edt_B           42 VATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRAL  112 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            4568899999999999999999999998754      3334 34588888899999999988  6665554

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=93.89  E-value=0.27  Score=28.51  Aligned_cols=60  Identities=7%  Similarity=-0.166  Sum_probs=30.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCH--hhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNA--VTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~--~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..|..+-..|.+.|++++|+..|++....+-.|+.  ..|..+-..+...|+.++  ..++...
T Consensus        38 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~  101 (272)
T 3u4t_A           38 YIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAV  101 (272)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            35555555666666666666666665542211111  124455555555555555  4444443

>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=93.82  E-value=0.22  Score=31.87  Aligned_cols=60  Identities=12%  Similarity=-0.027  Sum_probs=30.5

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+|..+-..|.+.|++++|...|++.....- -+...+..+-..+...|+.++  ..+....
T Consensus       310 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  371 (537)
T 3fp2_A          310 PPTYYHRGQMYFILQDYKNAKEDFQKAQSLNP-ENVYPYIQLACLLYKQGKFTESEAFFNETK  371 (537)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44555555555555556666655555554321 123345555555555555555  4444443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=93.82  E-value=0.35  Score=26.17  Aligned_cols=62  Identities=11%  Similarity=-0.057  Sum_probs=50.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|+..|.+..... ..+...|..+-.++...|+++.  ..|.....
T Consensus        62 ~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           62 NIPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            34688889999999999999999999988764 2256688888888999999988  66666554

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=93.78  E-value=0.33  Score=24.87  Aligned_cols=60  Identities=7%  Similarity=-0.127  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC----HhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN----AVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ..|..+-..|.+.|++++|...|++.....  |+    ...+..+-.++...|+.++  ..|+.....
T Consensus        40 ~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           40 NALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            366677778888899999999998887653  33    3456666677778888877  777766654

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=93.70  E-value=0.41  Score=28.59  Aligned_cols=63  Identities=14%  Similarity=0.072  Sum_probs=46.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+-..|.+.|++++|...|++..... ..+..++..+-..+...|+.++  ..++....
T Consensus       152 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~  216 (359)
T 3ieg_A          152 WDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLK  216 (359)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            356677888888888888888888888877553 2356677778888888888877  66665554

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=93.69  E-value=0.21  Score=29.35  Aligned_cols=63  Identities=21%  Similarity=0.056  Sum_probs=49.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc------CCCCC-HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR------GPRPN-AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~------g~~pd-~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ....|..+-..|.+.|++++|.++|++....      +-.|+ ..++..+-..+...|+.++  ..++....
T Consensus       152 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          152 VAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4467888899999999999999999998764      22443 3477888888999999988  66666553

>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=93.68  E-value=0.38  Score=25.27  Aligned_cols=58  Identities=10%  Similarity=-0.015  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+|.-+=..|.+.|++++|++.|.+..+.  .| +...|..+=.++.+.|++++  ..++...
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al   69 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAV   69 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHH
Confidence            45555656777888888888888887654  34 45577777777778888777  5554443

>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=93.45  E-value=0.26  Score=26.68  Aligned_cols=61  Identities=2%  Similarity=-0.175  Sum_probs=49.5

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|-.+=..|.+.|++++|++.|++..+..  | +...|..+-.++...|+.++  ..|+....
T Consensus        30 ~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~   93 (150)
T 4ga2_A           30 KSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ--ERDPKAHRFLGLLYELEENTDKAVECYRRSVE   93 (150)
T ss_dssp             HHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence            34556677788999999999999999988663  4 66788889999999999988  77776654

>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=93.45  E-value=0.25  Score=28.49  Aligned_cols=62  Identities=13%  Similarity=-0.072  Sum_probs=48.6

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc------CCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR------GPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~------g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...+|+.+-..|...|++++|...|.+....      .-.| ...++..+-..+...|++++  ..++...
T Consensus        84 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  154 (283)
T 3edt_B           84 VAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRAL  154 (283)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4568899999999999999999999998754      2223 35578888888999999988  6665554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=93.29  E-value=0.45  Score=25.00  Aligned_cols=60  Identities=13%  Similarity=0.060  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      -.|...=..|.+.|++++|++.|.+..+.. .-+...|..+-.++.+.|+.++  ..++....
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~   75 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIR   75 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHH
Confidence            456666677899999999999999987664 2367788888889999999988  66666554

>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=93.24  E-value=0.37  Score=30.80  Aligned_cols=59  Identities=8%  Similarity=-0.012  Sum_probs=44.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHH
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMG   64 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~   64 (87)
                      .+...|..+-..|.+.|++++|++.|++..... ..+...+..+-.++...|+.++  ..|.
T Consensus        57 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~  117 (537)
T 3fp2_A           57 NEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTDAMFDLS  117 (537)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            466788888888888888888888888887654 2256677777788888888877  5554

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=93.22  E-value=0.27  Score=31.83  Aligned_cols=54  Identities=9%  Similarity=-0.124  Sum_probs=44.5

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc-----C-CCCCHh-hHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR-----G-PRPNAV-TFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----g-~~pd~~-t~~~ll~~~~~~~~~~~   60 (87)
                      ..+++.+...|...|++++|+.++++...-     | -.|++. +++.+-..|...|+.++
T Consensus       329 ~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~e  389 (429)
T 3qwp_A          329 LKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQ  389 (429)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHH
Confidence            368999999999999999999999987632     2 445554 78888899999999887

>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=93.18  E-value=0.15  Score=27.05  Aligned_cols=59  Identities=7%  Similarity=0.027  Sum_probs=43.6

Q ss_pred             chhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhhccc
Q 042815           23 NGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQAAC   85 (87)
Q Consensus        23 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~~~~   85 (87)
                      .=+..+-++.+-...+.|+.....+.|+||-+..++..  ++++..+.+    ..+...+|..++
T Consensus        26 ~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K----~~~~~~iY~~~l   86 (109)
T 1v54_E           26 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK----AGPHKEIYPYVI   86 (109)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----TTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH----hcCchhhHHHHH
Confidence            34556666777777899999999999999999998888  888888876    333344555544

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=93.13  E-value=0.34  Score=32.01  Aligned_cols=54  Identities=6%  Similarity=-0.218  Sum_probs=44.5

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc-----C-CCCCHh-hHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR-----G-PRPNAV-TFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----g-~~pd~~-t~~~ll~~~~~~~~~~~   60 (87)
                      ..++|.|...|...|++++|+.++++..+-     | -.|++. +++.+-..|...|+.++
T Consensus       351 a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~e  411 (490)
T 3n71_A          351 LRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEV  411 (490)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHH
Confidence            368999999999999999999999997632     2 345544 88899999999999988

>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=93.12  E-value=0.37  Score=25.33  Aligned_cols=64  Identities=13%  Similarity=0.029  Sum_probs=43.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcC--CCCC----HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRG--PRPN----AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g--~~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|+.+=..|.+.|++++|++.|++..+..  ..++    ..+|..+=.++...|+++.  ..|+....
T Consensus        40 ~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           40 SNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            467889999999999999999999999977532  1111    1234444445556666766  66666554

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=93.03  E-value=0.55  Score=26.71  Aligned_cols=54  Identities=11%  Similarity=0.009  Sum_probs=36.1

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           13 MMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        13 li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +-..|.+.|++++|+..|++..+..  | +...+..+-..+...|+.++  ..|++...
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  116 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKA--PNNVDCLEACAEMQVCRGQEKDALRMYEKILQ  116 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6666777777777777777766553  3 45566666667777777766  56665543

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=92.79  E-value=0.68  Score=27.77  Aligned_cols=60  Identities=7%  Similarity=-0.163  Sum_probs=44.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh------hHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV------TFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~------t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+|+.+-..|.+.|++++|+..|++...........      .|..+-.++...|+.+.  ..|+...
T Consensus       159 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  226 (292)
T 1qqe_A          159 KCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQ  226 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            468888899999999999999999988654332221      45666667777888877  6666654

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=92.77  E-value=0.56  Score=27.12  Aligned_cols=60  Identities=12%  Similarity=0.103  Sum_probs=46.2

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+|..+-..|.+.|++++|+..|++..... .-+...+..+-..+...|+.++  ..++....
T Consensus        75 ~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  136 (272)
T 3u4t_A           75 ADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIR  136 (272)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhh
Confidence            347888888899999999999999887653 2245678888888888888887  67766654

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=92.70  E-value=0.92  Score=29.47  Aligned_cols=63  Identities=3%  Similarity=-0.079  Sum_probs=48.2

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCH--hhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNA--VTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~--~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+...+.+.|++++|..+|++..+.  .|+.  ..|........+.|.++.  .+|......
T Consensus       319 ~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~  385 (530)
T 2ooe_A          319 KNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  385 (530)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            35778899999999999999999999998864  5542  477777777777777777  677666543

>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=92.70  E-value=0.66  Score=25.29  Aligned_cols=30  Identities=0%  Similarity=-0.156  Sum_probs=16.9

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      +...|..+-..|...|++++|...|++...
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   72 (177)
T 2e2e_A           43 NSEQWALLGEYYLWQNDYSNSLLAYRQALQ   72 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344555555555566666666666655543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=92.41  E-value=0.57  Score=24.36  Aligned_cols=58  Identities=9%  Similarity=0.043  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .|-.+-..+.+.|++++|+..|++....  .| +...|..+=.++...|+.++  ..+++...
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   79 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARM   79 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4555667789999999999999998876  34 56677777788888899888  77776654

>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=92.36  E-value=0.76  Score=28.37  Aligned_cols=51  Identities=10%  Similarity=-0.071  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      .|..+-..|.+.|++++|+..|++..... ..+...+..+-.++...|++++
T Consensus       198 ~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~  248 (336)
T 1p5q_A          198 SHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFEL  248 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHH
Confidence            44444444555555555555555544332 1133344444444444444444

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=92.32  E-value=0.47  Score=23.21  Aligned_cols=52  Identities=12%  Similarity=0.079  Sum_probs=33.5

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCC-CHh-hHHHHHHHHcccchhHH--HHHHhchh
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRP-NAV-TFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~-t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ..+.+.|++++|...|++..+..  | +.. .+..+-.++...|+.++  ..|+....
T Consensus         8 ~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            8 KELINQGDIENALQALEEFLQTE--PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC--SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            34667778888888888776553  3 334 56666666667777766  55655543

>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=92.20  E-value=0.85  Score=25.44  Aligned_cols=60  Identities=8%  Similarity=-0.035  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ..|..+-..|.+.|++++|+..|++..... ..+...+..+-.++...|+.+.  ..|+....
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  150 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAAS  150 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            678888888999999999999999987663 2356677777788888888887  66666553

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=92.12  E-value=0.97  Score=27.94  Aligned_cols=59  Identities=7%  Similarity=-0.059  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .|+.+-..|.+.|++++|+..|++..... .-+...|..+-.++...|+++.  ..|+....
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            78888889999999999999999987653 2256788888889999999988  67776653

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=92.01  E-value=0.98  Score=29.06  Aligned_cols=62  Identities=6%  Similarity=-0.119  Sum_probs=48.2

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|.++-..+...|++++|...+++....+  |+...|..+=..+.-.|+.++  ..+++...
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Alr  338 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFN  338 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            456677777666777899999999999999886  787777676677778899888  66655543

>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=91.99  E-value=0.92  Score=27.98  Aligned_cols=63  Identities=10%  Similarity=-0.058  Sum_probs=50.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH---HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV---TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~---~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|+..|++..+..  | +...+..+-.++.+.|+.++   ..+..|..+
T Consensus       228 ~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~~~  294 (336)
T 1p5q_A          228 NNEKGLSRRGEAHLAVNDFELARADFQKVLQLY--PNNKAAKTQLAVCQQRIRRQLAREKKLYANMFER  294 (336)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467789999999999999999999999988663  4 56677788888888888876   566666543

>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=91.97  E-value=0.76  Score=24.34  Aligned_cols=62  Identities=11%  Similarity=0.042  Sum_probs=48.8

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ...|..+-..|.+.|++++|...|.+..... ..+...+..+-..+...|+.++  ..+......
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~   76 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL   76 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4567888888999999999999999987653 2256678888888888898888  666666543

>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=91.89  E-value=0.92  Score=29.55  Aligned_cols=63  Identities=6%  Similarity=-0.070  Sum_probs=48.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+..+|+.+-..|.+.|++++|++.|++..+.. .-+...+..+-.++...|+.++  ..+++...
T Consensus        38 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~  102 (477)
T 1wao_1           38 SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVK  102 (477)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            356788888889999999999999999987653 1255677778888888888887  66666554

>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=91.85  E-value=1.1  Score=29.34  Aligned_cols=52  Identities=4%  Similarity=-0.138  Sum_probs=21.1

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~   60 (87)
                      ..|..+-..|.+.|++++|.+.|++..+.. .-+...+..+-.++.+.|+.++
T Consensus        58 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~  109 (568)
T 2vsy_A           58 EAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAGQAEA  109 (568)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHH
Confidence            344444444444444444444444443321 1123334444444444444443

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=91.81  E-value=0.62  Score=30.18  Aligned_cols=63  Identities=13%  Similarity=-0.081  Sum_probs=52.6

Q ss_pred             CcHhHHHHHHHHHHhcCCc-hhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKN-GMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~-~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|...|++ ++|++.|++..+..  | +...|..+-.++...|++++  ..|+.....
T Consensus       100 ~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~  166 (474)
T 4abn_A          100 VEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE--PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH  166 (474)
T ss_dssp             CCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            4667888888899999999 99999999988764  4 46788999999999999988  777777654

>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=91.77  E-value=1  Score=26.93  Aligned_cols=59  Identities=5%  Similarity=-0.150  Sum_probs=35.1

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      +...|..+-..|.+.|++++|...|++..+.  .| +...+..+-.++...|+.++  ..|...
T Consensus        37 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a   98 (281)
T 2c2l_A           37 VAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQLEMESYDEAIANLQRA   98 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4556666666666777777777777665533  33 34455556666666666665  444443

>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=91.46  E-value=1.4  Score=26.37  Aligned_cols=61  Identities=15%  Similarity=-0.014  Sum_probs=49.8

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|+..|.+....  .| +...|..+-.++.+.|++++  ..++....
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~   66 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALE   66 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            5567888888999999999999999998866  34 66788888888889999988  66666554

>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=91.15  E-value=1.5  Score=27.90  Aligned_cols=70  Identities=10%  Similarity=-0.099  Sum_probs=50.7

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc--ccccccchhhh
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN--LWYYIDGQIDA   80 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~--~~~g~~~~~~~   80 (87)
                      ...++..+...|+.+++...+....... .-+...+..+|.++...|+..+  ..|+.....  ...|++|+..+
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            3456777888999999998888876553 2377799999999999998877  555554332  11578887654

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=91.13  E-value=1.1  Score=28.08  Aligned_cols=65  Identities=6%  Similarity=-0.092  Sum_probs=49.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ++..++..+-..|...|++++|++++.+-...|-.+ +...+...+..+.+.|+++.  ..++.|...
T Consensus        98 ~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~  165 (310)
T 3mv2_B           98 NSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA  165 (310)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            445555677788899999999999999875544212 55578888889999999988  888887643

>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=90.87  E-value=1  Score=31.16  Aligned_cols=59  Identities=10%  Similarity=-0.017  Sum_probs=32.8

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+|+.|=..|.+.|++++|++.|++..+.  .| +...+..+=.++.+.|+.++  ..|++..
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al   70 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAI   70 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            445666666666666666666666665543  23 23455555555666666655  4444443

>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=90.63  E-value=1.3  Score=27.88  Aligned_cols=61  Identities=8%  Similarity=-0.005  Sum_probs=49.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|+.+-..|.+.|++++|++.|++..+.  .| +...+..+-.++...|+.++  ..++....
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~  335 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEI--DPSNTKALYRRAQGWQGLKEYDQALADLKKAQE  335 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            4567888889999999999999999998764  45 56678888888889999888  66666554

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=90.58  E-value=0.96  Score=22.98  Aligned_cols=56  Identities=20%  Similarity=0.194  Sum_probs=42.0

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHHcCCCCCH----hhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           12 AMMLGLAKNGKNGMGVELFMSIEKRGPRPNA----VTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        12 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~----~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+-..+.+.|++++|...|++.....  |+.    ..+..+-.++...|+.++  ..|+.....
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~   68 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSR   68 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34566788999999999999988653  333    366667777888899888  777776654

>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=90.53  E-value=0.42  Score=26.74  Aligned_cols=56  Identities=7%  Similarity=0.066  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccchhhhhhccc
Q 042815           26 GVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDGQIDAWQAAC   85 (87)
Q Consensus        26 a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~~~~~~~~~~   85 (87)
                      ..+-++.+....+.|+.....+.|++|-+..++..  ++++..+.+    ..+....|..++
T Consensus        72 lrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K----~~~~~~iY~y~l  129 (152)
T 2y69_E           72 LRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK----AGPHKEIYPYVI  129 (152)
T ss_dssp             HHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----TTTCTTHHHHHH
T ss_pred             HHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh----cCCchhhHHHHH
Confidence            33444455567799999999999999999999988  999988876    334455565544

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=90.52  E-value=0.77  Score=22.61  Aligned_cols=36  Identities=14%  Similarity=0.141  Sum_probs=29.9

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCH
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNA   42 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~   42 (87)
                      .+...|..+-..|.+.|++++|++.|++....  .|+.
T Consensus        36 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~   71 (111)
T 2l6j_A           36 QNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTA   71 (111)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSST
T ss_pred             CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCc
Confidence            36678888999999999999999999998754  5553

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=90.38  E-value=1.3  Score=26.52  Aligned_cols=55  Identities=16%  Similarity=0.180  Sum_probs=35.7

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~   60 (87)
                      |...+..+-..|.+.|++++|++.|.+.....-.. +...+..+...+...|+.+.
T Consensus       218 ~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  273 (287)
T 3qou_A          218 DAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDA  273 (287)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCH
T ss_pred             cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCc
Confidence            45566777777777777777777777777653221 24466666666666666554

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=90.34  E-value=1.7  Score=25.29  Aligned_cols=63  Identities=16%  Similarity=0.087  Sum_probs=48.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC----HhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN----AVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...+-..-..+.+.|++++|...|++.....  |+    ...+..+-.++.+.|+.+.  ..|+.....
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   81 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQI   81 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence            455666677778899999999999999998653  43    4566677778888899888  777777654

>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=90.01  E-value=1.4  Score=23.92  Aligned_cols=63  Identities=5%  Similarity=-0.099  Sum_probs=47.7

Q ss_pred             cHhHHHHHHHH-HHhcCCc--hhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLG-LAKNGKN--GMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~-~~~~g~~--~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      +...|..+-.. |.+.|++  ++|...|++.....- -+...+..+-..+...|+.+.  ..+......
T Consensus        77 ~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           77 NAELYAALATVLYYQASQHMTAQTRAMIDKALALDS-NEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            55667777777 7789998  999999999887641 245677777788888898888  677766543

>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=89.99  E-value=1.4  Score=28.96  Aligned_cols=63  Identities=8%  Similarity=-0.073  Sum_probs=51.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|..+-..|.+.|++++|.+.|++..+.  .| +...+..+-..+...|+.++  ..+++....
T Consensus        21 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   86 (568)
T 2vsy_A           21 QDFVAWLMLADAELGMGDTTAGEMAVQRGLAL--HPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDA   86 (568)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            35678899999999999999999999998765  44 56688888888999999988  777766543

>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=89.71  E-value=0.75  Score=27.46  Aligned_cols=59  Identities=19%  Similarity=0.039  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHH----c-CCCCCHh-hHHHHHHHHcccchhHH--HHHHhc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEK----R-GPRPNAV-TFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~----~-g~~pd~~-t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      .+|+.+-..|.+.|++++|+..|++..+    . +..|... ++..+-..|.+.|+.++  ..++..
T Consensus       156 ~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~a  222 (293)
T 3u3w_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKA  222 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            3689999999999999999999999873    1 2233333 77888888889999888  555443

>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=89.52  E-value=1.1  Score=28.42  Aligned_cols=27  Identities=7%  Similarity=-0.101  Sum_probs=11.6

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIE   34 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~   34 (87)
                      ..|+.+-..|.+.|++++|+..|++..
T Consensus       167 ~a~~~~g~~~~~~g~~~eAl~~~~kal  193 (382)
T 2h6f_A          167 QVWHHRRVLVEWLRDPSQELEFIADIL  193 (382)
T ss_dssp             HHHHHHHHHHHHHTCCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            334444444444444444444444443

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=89.43  E-value=1  Score=28.14  Aligned_cols=62  Identities=8%  Similarity=-0.024  Sum_probs=44.4

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-----CHhhHHHHHHHHccc--c--hhHH--HHHHhchhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-----NAVTFVGVLTAYGKI--K--IFGV--TLMGIQPQN   69 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-----d~~t~~~ll~~~~~~--~--~~~~--~~~~~m~~~   69 (87)
                      +...+-.++..|.+.|+.+.|.+.+++|.+.  .|     +..+..-+..++...  |  +...  .+|+++..+
T Consensus       135 ~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~  207 (310)
T 3mv2_B          135 TTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT  207 (310)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh
Confidence            5567778888899999999999999998765  56     356666666663332  2  5555  888887655

>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=88.94  E-value=2.1  Score=29.72  Aligned_cols=23  Identities=13%  Similarity=-0.013  Sum_probs=9.0

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHH
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMS   32 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~   32 (87)
                      |+.+=..|.+.|++++|++.|++
T Consensus        80 ~~nLg~~l~~~g~~~~A~~~~~k  102 (723)
T 4gyw_A           80 YSNMGNTLKEMQDVQGALQCYTR  102 (723)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            33333333333444444444333

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=88.81  E-value=2.1  Score=24.41  Aligned_cols=63  Identities=13%  Similarity=0.087  Sum_probs=44.9

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCC-CC-HhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPR-PN-AVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-pd-~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ...+-.+-..+.+.|++++|...|+++....-. |. ...+..+-.++-+.|+.++  ..|+.....
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   70 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   70 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            344555666788899999999999998865321 21 2456667778888888888  777776654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=88.75  E-value=1.1  Score=21.12  Aligned_cols=32  Identities=13%  Similarity=0.096  Sum_probs=27.8

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      .+...|..+-..|.+.|++++|...|++....
T Consensus        41 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A           41 NNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            35677888889999999999999999998765

>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=88.68  E-value=0.96  Score=28.85  Aligned_cols=41  Identities=5%  Similarity=0.098  Sum_probs=34.8

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHH-----cCCCCCHhhHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEK-----RGPRPNAVTFV   46 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~g~~pd~~t~~   46 (87)
                      +...|-.+|.+|.+.|+..+|++.|++...     .|+.|...+-.
T Consensus       204 ~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          204 REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            556899999999999999999999999754     49999877543

>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=88.33  E-value=4  Score=28.18  Aligned_cols=77  Identities=10%  Similarity=-0.044  Sum_probs=56.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccch---hHH--HHHHhchhcccccccchhh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKI---FGV--TLMGIQPQNLWYYIDGQID   79 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~---~~~--~~~~~m~~~~~~g~~~~~~   79 (87)
                      .|..+|..+|..+.+.+.++++..+|+++... ......-|.-.+..-.+.+.   ++.  .+|++....  ....|++.
T Consensus        64 ~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~--~~~~~sv~  140 (679)
T 4e6h_A           64 TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSK--ELGNNDLS  140 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCS--SSCCCCHH
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHh--cCCCCCHH
Confidence            47889999999999999999999999999865 23345567777777777777   766  888888865  11136666


Q ss_pred             hhhcc
Q 042815           80 AWQAA   84 (87)
Q Consensus        80 ~~~~~   84 (87)
                      .|..-
T Consensus       141 LW~~Y  145 (679)
T 4e6h_A          141 LWLSY  145 (679)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66543

>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=88.29  E-value=2.6  Score=27.20  Aligned_cols=60  Identities=10%  Similarity=-0.148  Sum_probs=38.7

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...|+.+-..|.+.|++++|+..|++..... .-+...|..+-.++...|++++  ..|+...
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al  378 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVL  378 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            4566677777777777777777777766543 1245566666666667777666  5555544

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=87.69  E-value=1.4  Score=24.12  Aligned_cols=63  Identities=6%  Similarity=-0.058  Sum_probs=45.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .....|+.+-..|...|++++|...|++....    +..| ....+..+-..+...|++++  ..++...
T Consensus        24 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al   93 (203)
T 3gw4_A           24 TASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEER   93 (203)
T ss_dssp             THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45678888989999999999999999997651    2222 33466666777778888887  5555433

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=87.56  E-value=2.1  Score=26.35  Aligned_cols=60  Identities=8%  Similarity=-0.066  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+|+.+=..|.+.|++++|...|++....    +-.| ...++..+-..+.+.|+.++  ..++...
T Consensus       225 ~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  291 (383)
T 3ulq_A          225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGM  291 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            47788888899999999999999987652    3323 34477778888888888877  5555443

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=87.51  E-value=2.3  Score=24.84  Aligned_cols=58  Identities=16%  Similarity=0.154  Sum_probs=40.9

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC-----HhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN-----AVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-----~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      ...+...-..+.+.|++++|..+|++.....  |+     ...+..+-..+...|+++.  ..++..
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a   69 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHD   69 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3445555566788899999999999988763  33     3566677777888888877  555543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=87.44  E-value=3.3  Score=26.02  Aligned_cols=60  Identities=15%  Similarity=0.073  Sum_probs=45.0

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc-------CCCC-CHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR-------GPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-------g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      ...||.|=..|...|++++|++.|++-.+-       ...| ...+|..+-..+...|+.++  ..++..
T Consensus        51 a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka  120 (472)
T 4g1t_A           51 ATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKV  120 (472)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            457888888889999999999999885431       1233 34688888889999999888  555443

>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=87.24  E-value=2.6  Score=23.72  Aligned_cols=61  Identities=7%  Similarity=-0.175  Sum_probs=46.1

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc-----CCCCCHh-hH----HHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR-----GPRPNAV-TF----VGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----g~~pd~~-t~----~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...|+.+=.++.+.|++++|+..|++-...     .+.||-. .|    ...=.++...|+.++  ..|+...
T Consensus        57 a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAl  129 (159)
T 2hr2_A           57 AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  129 (159)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHH
Confidence            348999999999999999999999998764     2367543 66    666677778888887  5555443

>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=86.97  E-value=2.8  Score=24.94  Aligned_cols=58  Identities=5%  Similarity=-0.102  Sum_probs=40.2

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHcCCC-CC----HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSIEKRGPR-PN----AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +..+...|...|++++|+..|++....... +|    ..+++.+-..+...|+.++  ..|+...
T Consensus       118 ~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al  182 (293)
T 3u3w_A          118 QYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQIL  182 (293)
T ss_dssp             HHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334666666778899999999998763322 23    2257788888888888887  6666555

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=86.89  E-value=1.1  Score=23.15  Aligned_cols=61  Identities=8%  Similarity=-0.120  Sum_probs=40.3

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCC-CCC----HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGP-RPN----AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~pd----~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+|..+-..|...|++++|...|++.....- .++    ..++..+-..+...|+.++  ..++...
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~   76 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTL   76 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34677777888889999999999988764311 111    1356666667777787777  5555443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=86.88  E-value=3.7  Score=24.95  Aligned_cols=60  Identities=15%  Similarity=0.148  Sum_probs=44.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC-----HhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN-----AVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-----~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      .....+...=..+.+.|++++|..+|++.....  |+     ...+..+-..+...|+++.  ..++..
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a   73 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHD   73 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            455666677778889999999999999988763  33     2467777778888888877  555543

>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=86.83  E-value=2.8  Score=27.04  Aligned_cols=63  Identities=8%  Similarity=-0.088  Sum_probs=45.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH---HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV---TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~---~~~~~m~~~   69 (87)
                      .+...|..+-.+|.+.|++++|+..|++..+.  .| +...+..+-.++.+.++.++   ..+..|..+
T Consensus       349 ~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f~k  415 (457)
T 1kt0_A          349 ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERDRRIYANMFKK  415 (457)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46778889999999999999999999998754  45 44577777777777777765   566666543

>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=86.71  E-value=4.2  Score=25.47  Aligned_cols=73  Identities=5%  Similarity=-0.132  Sum_probs=53.6

Q ss_pred             HhHHHHHHHHHHh-----cCCchhHHHHHHHHHHcCCCC--CHhhHHHHHHHHccc-chhHH--HHHHhchhccccccc-
Q 042815            7 ATTSSAMMLGLAK-----NGKNGMGVELFMSIEKRGPRP--NAVTFVGVLTAYGKI-KIFGV--TLMGIQPQNLWYYID-   75 (87)
Q Consensus         7 ~~~~~~li~~~~~-----~g~~~~a~~l~~~m~~~g~~p--d~~t~~~ll~~~~~~-~~~~~--~~~~~m~~~~~~g~~-   75 (87)
                      -..|..+-.-|.+     -|+.++|.+.|++-.+-  .|  +..++...-+.++.. ++.+.  ..+++....   ... 
T Consensus       199 GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~L--nP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a---~p~~  273 (301)
T 3u64_A          199 GAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRY--CSAHDPDHHITYADALCIPLNNRAGFDEALDRALAI---DPES  273 (301)
T ss_dssp             HHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHH--CCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHC---CGGG
T ss_pred             CHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHh--CCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcC---CCCC
Confidence            4688999999999     49999999999997765  45  356777778888874 77666  777776654   343 


Q ss_pred             -chhhhhhcc
Q 042815           76 -GQIDAWQAA   84 (87)
Q Consensus        76 -~~~~~~~~~   84 (87)
                       |+....|..
T Consensus       274 ~P~~~lan~~  283 (301)
T 3u64_A          274 VPHNKLLVIL  283 (301)
T ss_dssp             CSSCHHHHHH
T ss_pred             CCChhHHHHH
Confidence             666655543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=86.67  E-value=2  Score=21.74  Aligned_cols=47  Identities=17%  Similarity=0.219  Sum_probs=33.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcC-CCCCHhhHHHHHHHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRG-PRPNAVTFVGVLTAY   52 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t~~~ll~~~   52 (87)
                      +...|..+-..|.+.|++++|+..|++..... -.|+...|...+..+
T Consensus        60 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~ai~~~  107 (117)
T 3k9i_A           60 HQALRVFYAMVLYNLGRYEQGVELLLKIIAETSDDETIQSYKQAILFY  107 (117)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHTHHHHHHH
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            56778889999999999999999999987542 233333444444333

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=86.54  E-value=3  Score=24.78  Aligned_cols=61  Identities=16%  Similarity=0.024  Sum_probs=45.8

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc-CCCCC-----HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR-GPRPN-----AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-g~~pd-----~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+|+.+-..|.+.|++++|...|++.... ...|+     ..++..+-..|.+.|+.++  ..++...
T Consensus       155 ~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal  223 (293)
T 2qfc_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAI  223 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHH
Confidence            348899999999999999999999997621 11222     2578888888999999988  5555543

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=86.33  E-value=2.1  Score=22.11  Aligned_cols=60  Identities=10%  Similarity=-0.036  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcC----CCCC-HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRG----PRPN-AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g----~~pd-~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .++..+-..|...|++++|.+.|++.....    -.+. ...+..+-..+...|+.++  ..++...
T Consensus        50 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  116 (164)
T 3ro3_A           50 IAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHL  116 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            478888888999999999999999976431    1111 3356666667777888877  5554443

>2b7e_A PRE-mRNA processing protein PRP40; structural protein; NMR {Saccharomyces cerevisiae} SCOP: a.159.2.1

Probab=86.25  E-value=1.3  Score=20.94  Aligned_cols=34  Identities=9%  Similarity=0.130  Sum_probs=27.0

Q ss_pred             chhHHHHHHHHHHcCCCCCHhhHHHHHHHH-cccc
Q 042815           23 NGMGVELFMSIEKRGPRPNAVTFVGVLTAY-GKIK   56 (87)
Q Consensus        23 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~-~~~~   56 (87)
                      .++|.+.|.+|+...-.+...||.-.++.+ ++..
T Consensus         2 ~eEae~aF~~lL~~~~V~s~wsweqamr~i~i~DP   36 (59)
T 2b7e_A            2 AMEAEKEFITMLKENQVDSTWSFSRIISELGTRDP   36 (59)
T ss_dssp             TTHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHCT
T ss_pred             hhHHHHHHHHHHHHcCCCCCCcHHHHHHHhccCCC
Confidence            478999999999665566778999999998 5543

>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=86.20  E-value=3.4  Score=23.99  Aligned_cols=14  Identities=0%  Similarity=0.041  Sum_probs=5.5

Q ss_pred             cCCchhHHHHHHHH
Q 042815           20 NGKNGMGVELFMSI   33 (87)
Q Consensus        20 ~g~~~~a~~l~~~m   33 (87)
                      .|++++|...|++.
T Consensus        55 ~~~~~~A~~~~~~a   68 (273)
T 1ouv_A           55 EKNLKKAASFYAKA   68 (273)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            33333333333333

>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=86.15  E-value=2.4  Score=25.55  Aligned_cols=61  Identities=7%  Similarity=-0.100  Sum_probs=39.3

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCCCHh-hHHHHHHHHcccchhHH--HHHHhch
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRPNAV-TFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~pd~~-t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+|+.+-..|.+.|++++|+..|++....    +..++.. .+..+..++...|+.+.  ..|+...
T Consensus       155 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          155 AELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            356777788888889999999988887642    2222222 45555555666677766  5565554

>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=86.13  E-value=3  Score=26.45  Aligned_cols=51  Identities=6%  Similarity=-0.051  Sum_probs=24.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccch-hHH
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKI-FGV   60 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~-~~~   60 (87)
                      ..|+.+-..+.+.|++++|++.|++....  .| +...|..+-..+...|+ +++
T Consensus        98 ~a~~~lg~~~~~~g~~~~Al~~~~~al~l--~P~~~~a~~~~g~~l~~~g~d~~e  150 (382)
T 2h6f_A           98 DVYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHE  150 (382)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcccCHHH
Confidence            34444444555555555555555554433  22 23344444444444453 444

>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=85.49  E-value=3.8  Score=23.81  Aligned_cols=57  Identities=5%  Similarity=-0.074  Sum_probs=28.4

Q ss_pred             hHHHHHHHHHHh----cCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcc----cchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAK----NGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGK----IKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~----~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~----~~~~~~--~~~~~m~   67 (87)
                      .+|..+-..|.+    .|++++|+..|++..+.+   +...+..+-..+..    .++.++  ..|+...
T Consensus        75 ~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~  141 (273)
T 1ouv_A           75 NGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKAC  141 (273)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHH
Confidence            344455555555    566666666666655443   33444444444444    444444  4444433

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=85.07  E-value=4.4  Score=24.20  Aligned_cols=59  Identities=7%  Similarity=-0.034  Sum_probs=43.1

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      -.+-.+-..+.+.|++++|...|++....  .| +...+..+-..+...|+.++  ..++....
T Consensus       118 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~  179 (287)
T 3qou_A          118 ELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPL  179 (287)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCG
T ss_pred             hhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCch
Confidence            34455566678889999999999988765  34 45577777788888888887  66766654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=84.95  E-value=1.9  Score=23.61  Aligned_cols=62  Identities=8%  Similarity=-0.061  Sum_probs=41.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCC--CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRP--NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p--d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ...+++.+-..|...|++++|.+.|.+....    +-.|  ....+..+-..+...|++++  ..++...
T Consensus        65 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  134 (203)
T 3gw4_A           65 EHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSL  134 (203)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3457777888888999999999999886643    2122  12346666666777788777  5554443

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=84.70  E-value=2.6  Score=26.01  Aligned_cols=60  Identities=15%  Similarity=0.094  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+++.+=..|.+.|++++|.+.|.+....    +-.....++..+-..+.+.|+.++  ..++...
T Consensus       223 ~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  288 (378)
T 3q15_A          223 ISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGL  288 (378)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            46677777788888888888888887651    212234566777777778888777  5555443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=84.67  E-value=2.2  Score=21.11  Aligned_cols=30  Identities=3%  Similarity=-0.102  Sum_probs=26.5

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHH
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEK   35 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~   35 (87)
                      +...|..+-..|.+.|++++|.+.|++...
T Consensus        40 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A           40 YVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            556889999999999999999999998764

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=83.79  E-value=2.1  Score=26.02  Aligned_cols=54  Identities=7%  Similarity=-0.038  Sum_probs=33.0

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHc----CCCCC-HhhHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKR----GPRPN-AVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~pd-~~t~~~ll~~~~~~~~~~~   60 (87)
                      ..+|..+-..|.+.|++++|...|++....    +-.+. ..++..+-..+...|+.++
T Consensus       267 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  325 (406)
T 3sf4_A          267 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQ  325 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHH
Confidence            346667777777777777777777776532    11111 3355566666666676666

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=83.75  E-value=1.8  Score=25.36  Aligned_cols=25  Identities=0%  Similarity=-0.073  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHH
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSI   33 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m   33 (87)
                      ++..+-..|.+.|++++|...|++.
T Consensus       265 ~~~~la~~~~~~g~~~~A~~~~~~a  289 (338)
T 3ro2_A          265 SCYSLGNTYTLLQDYEKAIDYHLKH  289 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            3444444444455555555544443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=83.65  E-value=5.4  Score=24.58  Aligned_cols=61  Identities=7%  Similarity=-0.150  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh--hHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV--TFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~--t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+..+=.++.+.|++++|+..|++.......|...  .....--++.+.|+.++  .+|+++...
T Consensus       173 a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          173 AGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            45555566888889999999888876433325422  33444455667777777  778777654

>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=83.27  E-value=3.5  Score=28.07  Aligned_cols=62  Identities=6%  Similarity=-0.183  Sum_probs=44.8

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|++.|++..+.. .-+...|..+=.++...|++++  ..|++...
T Consensus       432 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  495 (681)
T 2pzi_A          432 SVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLTGDYDSATKHFTEVLD  495 (681)
T ss_dssp             CSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45677777788888899999999988887653 1245566666677778888877  66666554

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=82.59  E-value=5.4  Score=24.46  Aligned_cols=58  Identities=14%  Similarity=0.104  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC-H----hhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN-A----VTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~----~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+..+-..+.+.|++++|..+|++..+.+  |+ .    ..+..+-..+...|+.+.  ..++...
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  113 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAG--TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDL  113 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            344555667888999999999999988763  33 2    367777777888888877  5555443

>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=81.65  E-value=4  Score=25.64  Aligned_cols=54  Identities=11%  Similarity=0.025  Sum_probs=39.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~   60 (87)
                      .+...|..+-.+|.+.|++++|+..|++..+.  .| +...+..+-..+...++.++
T Consensus       305 ~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~  359 (370)
T 1ihg_A          305 SNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKD  359 (370)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHH
Confidence            46778889999999999999999999998765  34 44455555555555555443

>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=81.08  E-value=5.2  Score=22.11  Aligned_cols=62  Identities=10%  Similarity=-0.087  Sum_probs=44.8

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCC-CCC--------------HhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGP-RPN--------------AVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~pd--------------~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ...|..+-..|.+.|++++|...|.+.....- .|+              ...+..+-.++...|+.++  ..+.....
T Consensus        38 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~  116 (198)
T 2fbn_A           38 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLK  116 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            34567777788899999999999999875421 121              2577777778888888887  66665554

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=80.61  E-value=3.8  Score=20.46  Aligned_cols=32  Identities=9%  Similarity=-0.098  Sum_probs=27.4

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      .+...|..+-..|.+.|++++|...|++....
T Consensus        51 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   82 (115)
T 2kat_A           51 TYSVAWKWLGKTLQGQGDRAGARQAWESGLAA   82 (115)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            35678888999999999999999999997653

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=80.31  E-value=2.4  Score=26.10  Aligned_cols=60  Identities=10%  Similarity=-0.021  Sum_probs=40.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcC--CC---CCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRG--PR---PNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g--~~---pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..|..+-..|.+.|++++|...|++.....  ..   ....++..+-..+...|+.++  ..++...
T Consensus       264 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  330 (411)
T 4a1s_A          264 RANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHL  330 (411)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            367778888888888888888888765431  11   114466677777777787777  5555443

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=80.23  E-value=4.2  Score=24.25  Aligned_cols=63  Identities=5%  Similarity=-0.107  Sum_probs=46.6

Q ss_pred             HhHHHHHHHHHHhc-CCchhHHHHHHHHHHcC--C-CC-C-HhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            7 ATTSSAMMLGLAKN-GKNGMGVELFMSIEKRG--P-RP-N-AVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         7 ~~~~~~li~~~~~~-g~~~~a~~l~~~m~~~g--~-~p-d-~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ..+|+.+-..|.+. |++++|+..|++.....  . .+ . ..++..+-..+...|+.++  ..|+.....
T Consensus       117 a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  187 (292)
T 1qqe_A          117 ANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKS  187 (292)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            34788888889986 99999999999976431  1 11 1 3467788888899999988  777776653

---

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	87
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.24
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.68
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	95.51
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	95.43
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.4
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	95.09
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	94.77
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	94.69
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	94.3
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	94.28
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	94.16
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	94.09
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	94.01
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	93.99
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	93.95
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	93.48
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	93.1
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	92.68
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	92.59
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	92.57
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	92.4
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	92.12
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	91.83
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	91.22
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	90.84
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	89.89
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	89.51
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	88.54
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	88.47
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	88.14
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	87.91
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	87.74
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	86.91
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	83.96
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	82.66
d1peqa1	162	R1 subunit of ribonucleotide reductase, N-terminal	81.19
d1u9pa1	36	Arc repressor {Salmonella bacteriophage P22 [TaxId	80.19

>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=97.24  E-value=0.0011  Score=36.70  Aligned_cols=72  Identities=10%  Similarity=-0.100  Sum_probs=58.0

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc--ccccccchhhh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN--LWYYIDGQIDA   80 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~--~~~g~~~~~~~   80 (87)
                      ..|..+...+.+.|++++|+..+++..... .-|...|..++.++...|+..+  ..|++....  ...|++|+..+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            467889999999999999999999998764 2378899999999999999998  777775332  11488887654

>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=95.68  E-value=0.012  Score=32.27  Aligned_cols=40  Identities=5%  Similarity=0.115  Sum_probs=35.0

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHH-----HcCCCCCHhh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIE-----KRGPRPNAVT   44 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~-----~~g~~pd~~t   44 (87)
                      -|...|..++.+|.+.|+.++|++.|+++.     +.|+.|...+
T Consensus        99 ~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          99 YREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            467899999999999999999999999974     3699998765

>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=95.51  E-value=0.055  Score=28.43  Aligned_cols=63  Identities=6%  Similarity=-0.070  Sum_probs=48.3

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|..+-..|.+.|++++|...|.+..+.. .-+...|..+-.++...|+.++  ..+++...
T Consensus        42 ~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~  106 (159)
T d1a17a_          42 SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVK  106 (159)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            466788888888999999999999999887664 2244688888888888888887  55655554

>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=95.43  E-value=0.055  Score=27.15  Aligned_cols=63  Identities=11%  Similarity=-0.080  Sum_probs=49.9

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+...|+.+=..|.+.|++++|+..|.+..... ..+...|..+-.++...|+.++  ..|+....
T Consensus        35 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~   99 (117)
T d1elwa_          35 HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLK   99 (117)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             cchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            356778888888999999999999999988665 3366788888888888888888  66666654

>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=95.40  E-value=0.055  Score=26.97  Aligned_cols=51  Identities=10%  Similarity=0.086  Sum_probs=32.0

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      ..+.+.|++++|+..|++.....  | +...|..+-.++.+.|+.++  ..+....
T Consensus        24 ~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al   77 (112)
T d1hxia_          24 LSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHAR   77 (112)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhccccccc
Confidence            34566777777777777766553  3 45566666666666777666  5555444

>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=95.09  E-value=0.07  Score=28.55  Aligned_cols=61  Identities=5%  Similarity=-0.175  Sum_probs=45.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .+...|+.+-..|.+.|++++|+..|.+..+  +.| +..+|..+-.++...|++++  ..|+...
T Consensus        36 ~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          36 LVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4667788888888888888888888888653  456 45577778888888888877  5555443

>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=94.77  E-value=0.13  Score=29.84  Aligned_cols=65  Identities=3%  Similarity=-0.084  Sum_probs=40.5

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .+...|......+.+.|++++|..+|+++...........|...+..+.+.|.++.  .+|......
T Consensus        97 ~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~  163 (308)
T d2onda1          97 KNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  163 (308)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTS
T ss_pred             CCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHh
Confidence            34556666777777777777777777776643322223356666777666666665  666665543

>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=94.69  E-value=0.12  Score=27.48  Aligned_cols=63  Identities=13%  Similarity=-0.075  Sum_probs=47.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      |++-.....=..|.+.|++++|+..|.+..... .-+...|..+-.++.+.|+++.  ..|.....
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~   66 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALE   66 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH
Confidence            334444444567899999999999999987664 2366688888899999999988  77766653

>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=94.30  E-value=0.18  Score=27.46  Aligned_cols=64  Identities=8%  Similarity=-0.029  Sum_probs=50.0

Q ss_pred             CCCCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            2 MPPRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         2 m~~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      +.+|+...|..+=..|.+.|++++|++.|++-.+.. .-+...|..+=.++.+.|+.++  ..|+..
T Consensus        31 i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~~~~~kA   96 (192)
T d1hh8a_          31 VQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEA   96 (192)
T ss_dssp             SSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHHHHHHHH
Confidence            456777888889889999999999999999987654 2256678888888888898887  555554

>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=94.28  E-value=0.12  Score=29.65  Aligned_cols=61  Identities=7%  Similarity=-0.073  Sum_probs=46.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|..+-..|.+.|++++|...|++..+..  | +..++..+-..+.+.|++++  ..+.....
T Consensus        32 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~   95 (388)
T d1w3ba_          32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN--PLLAEAYSNLGNVYKERGQLQEAIEHYRHALR   95 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHhhhhccccccccccccccc
Confidence            56678888888889999999999999887653  4 45577778888888888877  55555544

>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=94.16  E-value=0.15  Score=28.15  Aligned_cols=62  Identities=13%  Similarity=-0.086  Sum_probs=42.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+..+|+.+=..|.+.|++++|+..|++..+..  | +..++..+-.++...|+.+.  ..|+....
T Consensus        69 ~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_          69 DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH--hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            356677788888888888888888888877653  3 34466666677777777766  55555443

>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=94.09  E-value=0.16  Score=26.60  Aligned_cols=61  Identities=8%  Similarity=-0.038  Sum_probs=50.3

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ..+|+.+-..|.+.|++++|++.+.+..... .-+.-.|-.+-.++...|+++.  ..|+....
T Consensus        67 ~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          67 ISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            3577888899999999999999999988664 2367799999999999999998  66666654

>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=94.01  E-value=0.093  Score=26.67  Aligned_cols=50  Identities=8%  Similarity=0.003  Sum_probs=29.0

Q ss_pred             HHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815           16 GLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus        16 ~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      .|.+.|++++|+..|.+..+.. ..+...+..+-.++...|+++.  ..+...
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~a   64 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKA   64 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHH
Confidence            4566666666666666666543 1245566666666666666665  444443

>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=93.99  E-value=0.19  Score=26.72  Aligned_cols=59  Identities=10%  Similarity=-0.083  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .+|+-+-..|.+.|++++|+..+++.....  | +...+..+-.++...|+++.  ..|+....
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~~--p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALELD--SNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhcc--ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            456777788899999999999999887663  4 66688888888888898888  66766654

>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=93.95  E-value=0.18  Score=28.95  Aligned_cols=60  Identities=10%  Similarity=0.008  Sum_probs=33.0

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC-HhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN-AVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +...+..+...|.+.|++++|+..|++..+.  .|+ ..++..+-.++.+.|+.++  ..|++..
T Consensus       304 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al  366 (388)
T d1w3ba_         304 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAI  366 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3445555556666666666666666664432  343 3345555556666666655  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=93.48  E-value=0.11  Score=27.14  Aligned_cols=53  Identities=11%  Similarity=0.073  Sum_probs=43.1

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ..|.+.|++++|+..|.+..+.. .-+...|..+-.++-..|+.++  ..|.....
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~   72 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIE   72 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHH
Confidence            45789999999999999988764 2266688888889999999988  77776654

>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=93.10  E-value=0.27  Score=28.01  Aligned_cols=52  Identities=8%  Similarity=-0.046  Sum_probs=28.1

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV   60 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~   60 (87)
                      ...|..+-..|.+.|++++|.+.|++..+.  .| +...+..+-.+|.+.|+.++
T Consensus       206 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~  258 (323)
T d1fcha_         206 YLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGAHRE  258 (323)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             ccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCCHHH
Confidence            445555555566666666666666655543  23 23345555555555555555

>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=92.68  E-value=0.44  Score=27.07  Aligned_cols=60  Identities=7%  Similarity=0.065  Sum_probs=40.2

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +..+|..+-..|.+.|++++|...|.+..+.  .| +...+..+...+...|+.++  ..+....
T Consensus        52 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  114 (323)
T d1fcha_          52 HMEAWQYLGTTQAENEQELLAISALRRCLEL--KPDNQTALMALAVSFTNESLQRQACEILRDWL  114 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHhhhcc--ccccccccccccccccccccccccccchhhHH
Confidence            4567777777788888888888888776654  23 44566666667777777766  5554443

>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=92.59  E-value=0.34  Score=25.48  Aligned_cols=62  Identities=6%  Similarity=-0.046  Sum_probs=48.3

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +...|+.+-..|.+.|++++|+..|.+..+.. .-+...|..+-.++...|+++.  ..|.....
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            34567777888999999999999999987553 2256688888888999999988  66666554

>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=92.57  E-value=0.27  Score=28.37  Aligned_cols=29  Identities=10%  Similarity=-0.036  Sum_probs=19.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKR   36 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~   36 (87)
                      ..|...+....+.|..++|.++|.+..+.
T Consensus       135 ~~w~~~~~~~~~~~~~~~ar~i~~~al~~  163 (308)
T d2onda1         135 LVYIQYMKFARRAEGIKSGRMIFKKARED  163 (308)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHh
Confidence            35667777677777777777777776544

>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=92.40  E-value=0.24  Score=24.58  Aligned_cols=53  Identities=13%  Similarity=-0.011  Sum_probs=41.9

Q ss_pred             HHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815           15 LGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus        15 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      ..+.+.|++++|+.+|.+..+.. .-+...|..+=.++-+.|+.++  ..+.....
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~   65 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVD   65 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHH
Confidence            34788999999999999988764 2366678888888889999988  66666654

>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=92.12  E-value=0.21  Score=25.36  Aligned_cols=63  Identities=11%  Similarity=0.064  Sum_probs=36.1

Q ss_pred             cHhHHHHHHHHHHhcCC---chhHHHHHHHHHHcCCCCCH-hhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            6 DATTSSAMMLGLAKNGK---NGMGVELFMSIEKRGPRPNA-VTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~---~~~a~~l~~~m~~~g~~pd~-~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      +..++..+-.++.+.++   +++|+.+|++.....-.|+. .++..+=.+|.+.|+.+.  ..|+....
T Consensus        32 ~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          32 SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            44555555555655443   34577777776654433332 255555666667777776  66666553

>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=91.83  E-value=0.14  Score=25.77  Aligned_cols=47  Identities=9%  Similarity=0.038  Sum_probs=37.8

Q ss_pred             chhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815           23 NGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus        23 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      .=+..+-++.+-...+.|......+.|+||-+..++..  ++++..+.+
T Consensus        22 ~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          22 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34555566667777889999999999999999998888  888888765

>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=91.22  E-value=0.43  Score=24.11  Aligned_cols=58  Identities=12%  Similarity=-0.067  Sum_probs=42.4

Q ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhH---H--HHHHhchhc
Q 042815           11 SAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFG---V--TLMGIQPQN   69 (87)
Q Consensus        11 ~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~---~--~~~~~m~~~   69 (87)
                      ..++..+...+++++|.+.|++....+ ..+..++..+-.++.+.++.+   +  .+++.....
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~   65 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPK   65 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhc
Confidence            457788889999999999999988765 235567777777777655443   3  667776643

>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=90.84  E-value=0.15  Score=25.84  Aligned_cols=63  Identities=14%  Similarity=0.088  Sum_probs=41.9

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh-------hHHHHHHHHcccchhHH--HHHHhch
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV-------TFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-------t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      +.+..+|..+-..|.+.|++++|+..|.+..+..- .+..       +|..+=..+...++++.  ..|+...
T Consensus        35 p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~-~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          35 PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR-ENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH-HSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            34678999999999999999999999999875321 1222       34444444455555555  5555443

>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=89.89  E-value=0.83  Score=24.95  Aligned_cols=60  Identities=10%  Similarity=-0.070  Sum_probs=48.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCC-CHhhHHHHHHHHcccchhHH--HHHHhchhc
Q 042815            8 TTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRP-NAVTFVGVLTAYGKIKIFGV--TLMGIQPQN   69 (87)
Q Consensus         8 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~~~~~~~~~~~--~~~~~m~~~   69 (87)
                      ..|..+=..|.+.|++++|++.|++....  .| +..+|..+=.++.+.|++++  ..|+.....
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~  100 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL  100 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH
Confidence            45666667889999999999999998865  44 55688888889999999998  777776653

>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=89.51  E-value=0.6  Score=22.83  Aligned_cols=60  Identities=8%  Similarity=0.030  Sum_probs=49.6

Q ss_pred             cHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhc
Q 042815            6 DATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         6 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      +...|..+-..|.+.|++++|+..|++..+.. .-+...+..+-..+...|+.++  +.+++.
T Consensus        49 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          49 REEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            67789999999999999999999999987664 2257788888899999999887  666553

>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=88.54  E-value=0.47  Score=22.61  Aligned_cols=33  Identities=9%  Similarity=0.118  Sum_probs=28.1

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCC
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPN   41 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd   41 (87)
                      ..+++.+=..|.+.|++++|+..|++..+.  .|+
T Consensus        46 ~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l--~P~   78 (95)
T d1tjca_          46 VSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPE   78 (95)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHHHHhhHHHhcCChHHHHHHHHHHHHh--CcC
Confidence            357888999999999999999999998865  454

>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=88.47  E-value=0.73  Score=26.75  Aligned_cols=52  Identities=8%  Similarity=-0.026  Sum_probs=21.3

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhH
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFG   59 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~   59 (87)
                      ..+|+.+-..+.+.|++++|++.|.++.+..- -+...|..+-..+...|+.+
T Consensus       112 ~~a~~~~~~~~~~l~~~~eAl~~~~kal~~dp-~n~~a~~~~~~~~~~~~~~~  163 (315)
T d2h6fa1         112 YQVWHHRRVLVEWLRDPSQELEFIADILNQDA-KNYHAWQHRQWVIQEFKLWD  163 (315)
T ss_dssp             HHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCT
T ss_pred             hhHHHHHhHHHHhhccHHHHHHHHhhhhhhhh-cchHHHHHHHHHHHHHHhhH
Confidence            33444444444444444444444444443211 12334444444444444433

>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=88.14  E-value=1  Score=23.59  Aligned_cols=58  Identities=10%  Similarity=-0.150  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhch
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQP   67 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~   67 (87)
                      .|+-+-..|.+.|++++|+..+.+..... ..+...|-..-.++...|+++.  ..|....
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al  125 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVL  125 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45555566777777777777777766543 2255566666667777777766  5555544

>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=87.91  E-value=1.1  Score=23.72  Aligned_cols=63  Identities=17%  Similarity=0.004  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchhcccccccc
Q 042815           10 SSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQNLWYYIDG   76 (87)
Q Consensus        10 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~~~~~g~~~   76 (87)
                      .+--++...+.|+-++-.++++++.+.+ +|+.....-+-.||-+.|..++  +++.+..++   |+.-
T Consensus        89 vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~---G~Ke  153 (161)
T d1wy6a1          89 VNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKK---GEKE  153 (161)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH---hHHH
Confidence            4455677788888899899999977755 7888888899999999999988  888888776   6643

>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=87.74  E-value=1.1  Score=23.47  Aligned_cols=64  Identities=6%  Similarity=-0.109  Sum_probs=42.7

Q ss_pred             CCcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh-hHHHHHHHHcccchhHH---HHHHhchhc
Q 042815            4 PRDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV-TFVGVLTAYGKIKIFGV---TLMGIQPQN   69 (87)
Q Consensus         4 ~~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~ll~~~~~~~~~~~---~~~~~m~~~   69 (87)
                      +.+..+|..+-.+|...|++++|...|.+....  .|+-. ....+-..-...+...+   ..+..|..+
T Consensus        95 p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~~~~~~~~~~~e~~kk~~~~~f~~  162 (168)
T d1kt1a1          95 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIFMCQKKAKEHNERDRRTYANMFKK  162 (168)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence            457788999999999999999999999998754  56544 44333333334443332   555555543

>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=86.91  E-value=0.39  Score=25.97  Aligned_cols=55  Identities=9%  Similarity=0.033  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhHHHHHHHHcccchhHH--HHHHhchh
Q 042815            9 TSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTFVGVLTAYGKIKIFGV--TLMGIQPQ   68 (87)
Q Consensus         9 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~~~~~~~~~~~--~~~~~m~~   68 (87)
                      .||- =..+...|++++|++.|.++.    .|+..+|..+=.++...|+++.  ..|.+...
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~   64 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSIN   64 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHH
Confidence            4554 334678899999999998753    5777888888888889999988  77776654

>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=83.96  E-value=1.2  Score=25.58  Aligned_cols=37  Identities=24%  Similarity=0.214  Sum_probs=26.6

Q ss_pred             CcHhHHHHHHHHHHhcCCchhHHHHHHHHHHcCCCCCHh
Q 042815            5 RDATTSSAMMLGLAKNGKNGMGVELFMSIEKRGPRPNAV   43 (87)
Q Consensus         5 ~~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~   43 (87)
                      .|...+..+...|+..|++++|...|++..+.  .|+..
T Consensus        28 ~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~   64 (264)
T d1zbpa1          28 KDASLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYL   64 (264)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGH
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcH
Confidence            46677778888888888888888888877654  45443

>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=82.66  E-value=1.8  Score=24.08  Aligned_cols=60  Identities=3%  Similarity=-0.150  Sum_probs=43.3

Q ss_pred             HhHHHHHHHHHHhcCCchhHHHHHHHHHH----cCCCCCHh-hHHHHHHHHcccchhHH--HHHHhc
Q 042815            7 ATTSSAMMLGLAKNGKNGMGVELFMSIEK----RGPRPNAV-TFVGVLTAYGKIKIFGV--TLMGIQ   66 (87)
Q Consensus         7 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~----~g~~pd~~-t~~~ll~~~~~~~~~~~--~~~~~m   66 (87)
                      ...+..+-..|...|++++|...|++...    .+..|+.. .+..+-..+...|+.++  ..+++.
T Consensus       251 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~A  317 (366)
T d1hz4a_         251 QGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDA  317 (366)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            34566677889999999999999998763    35555443 66667777888888887  555543

>d1peqa1 a.98.1.1 (A:13-174) R1 subunit of ribonucleotide reductase, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: R1 subunit of ribonucleotide reductase, N-terminal domain
superfamily: R1 subunit of ribonucleotide reductase, N-terminal domain
family: R1 subunit of ribonucleotide reductase, N-terminal domain
domain: R1 subunit of ribonucleotide reductase, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=81.19  E-value=0.85  Score=24.54  Aligned_cols=34  Identities=18%  Similarity=0.205  Sum_probs=27.1

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHHcCCCCCHhhH
Q 042815           12 AMMLGLAKNGKNGMGVELFMSIEKRGPRPNAVTF   45 (87)
Q Consensus        12 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~   45 (87)
                      .+++.+...|+.+.|.++++.|......|-+-|+
T Consensus       119 m~vAl~l~~~~~~~a~~~y~~~~~~~~~~aTPT~  152 (162)
T d1peqa1         119 TMVALTLAQGDETLATQLTDEMLSGRFQPATPTF  152 (162)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTSEEECHHHH
T ss_pred             HHHHHHHccCcHHHHHHHHHHHHhCCeeCCCcHh
Confidence            3455566678899999999999888888887776

>d1u9pa1 a.43.1.1 (A:72-107) Arc repressor {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: Ribbon-helix-helix
superfamily: Ribbon-helix-helix
family: Arc/Mnt-like phage repressors
domain: Arc repressor
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=80.19  E-value=1  Score=17.45  Aligned_cols=33  Identities=15%  Similarity=0.236  Sum_probs=23.8

Q ss_pred             hHHHHHHHHH-HcCCCCCHhhHHHHHHHHcccch
Q 042815           25 MGVELFMSIE-KRGPRPNAVTFVGVLTAYGKIKI   57 (87)
Q Consensus        25 ~a~~l~~~m~-~~g~~pd~~t~~~ll~~~~~~~~   57 (87)
                      +.+++.++.. ++|...|...|.-++..+-+.|.
T Consensus         2 evldlvrkvaeeng~s~ns~iy~~vmes~kkegr   35 (36)
T d1u9pa1           2 EVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR   35 (36)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHcCcchhHHHHHHHHHHHHHccC
Confidence            3455666654 56888888899888888877664